Cell culture methods to reduce acidic species

ABSTRACT

The instant invention relates to the field of protein production and purification, and in particular to compositions and processes for controlling the amount of acidic species expressed by host cells, as well as to compositions and processes for controlling the amount of acidic species present in purified preparations.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application claims priority to U.S. Provisional ApplicationNo. 61/636,511, filed on Apr. 20, 2012, the disclosure of which isincorporated by reference herein in its entirety.

1. INTRODUCTION

The instant invention relates to the field of protein production, and inparticular to compositions and processes for controlling the amount ofacidic species generated during expression of a protein of interest byhost cells, as well as the reduction of acidic species present in theclarified cell culture broth. In certain aspects of the invention,controlling the amount of acidic species generated during expression ofa protein of interest is achieved by modifying the culture media of thecells. In certain aspects of the invention, controlling the amount ofacidic species generated during expression of a protein of interest isachieved by modifying the culture process parameters. In certain aspectsof the invention, controlling the amount of acidic species of a proteinof interest is achieved by modifying a cell culture clarified harvestcomprising the protein of interest.

2. BACKGROUND OF THE INVENTION

The production of proteins for biopharmaceutical applications typicallyinvolves the use of cell cultures that are known to produce proteinsexhibiting varying levels of product-related substance heterogeneity.Such heterogeneity includes, but is not limited to, the presence ofacidic species. For example, in monoclonal antibody (mAb) preparations,such acidic species heterogeneities can be detected by various methods,such as WCX-10 HPLC (a weak cation exchange chromatography) or TEF(isoelectric focusing). In certain embodiments, the acidic speciesidentified using such techniques comprise a range of product-relatedimpurities such as antibody product fragments (e.g., Fc and Fabfragments), and/or post-translation modifications of the antibodyproduct, such as, deamidated and/or glycoslyated antibodies. However,because of their similar chemical characteristics to the antibodyproduct molecules, reduction of acidic species is a challenge inmonoclonal antibody purification. Control of acidic speciesheterogeneity is particularly advantageous in the context of cellculture processes used for commercially produced recombinantbio-therapeutics as such heterogeneity has the potential to impactstability.

3. SUMMARY OF THE INVENTION

The present invention is directed to compositions and methods thatcontrol (modulate or limit) acidic species heterogeneity in a populationof proteins. The presence of such acidic species corresponds toheterogeneity of the distribution of charged impurities, e.g., a mixtureof protein fragments (e.g., Fc and Fab fragments of antibodies), and/orpost-translation modifications of the proteins, such as, deamidatedand/or glycoslyated proteins, in the population of proteins, and suchheterogeneity particularly of interest when it arises in the context ofrecombinant protein production.

In certain embodiments, the acidic species heterogeneity arises fromdifferences in the amount and/or type of acidic species in a populationof proteins.

In certain embodiments, the acidic species heterogeneity is present in apopulation of proteins produced by cell culture. In certain embodiments,control is exerted over the amount of acidic species of protein producedby cell culture. In certain embodiments, the control is exerted over theamount of acidic species formed while the protein is present in a cellculture broth, while the culture is actively maintained or while thecells are removed. In certain embodiments, the protein is an antibody.

In certain embodiments, control over the amount of acidic speciesproduced by cell culture is exerted by employing certain mediacomponents during production of a protein, for example, an antibody, ofinterest. In certain embodiments, control over the amount of acidicspecies of protein produced by cell culture is exerted by supplementingthe media of cells expressing the protein of interest with one or moreamino acids. In certain embodiments, the one or more amino acids arearginine, lysine, ornithine, histidine or combinations thereof.

In certain embodiments, control over the amount of acidic species ofprotein produced by cell culture is exerted by supplementing the mediaof cells expressing the protein of interest with calcium, for example,by supplementing the media with calcium chloride dihydrate.

In certain embodiments, control over the amount of acidic species ofprotein produced by cell culture is exerted by supplementing the mediaof cells expressing the protein of interest with vitamin niacinamide.

In certain embodiments, control over the amount of acidic species ofprotein produced by cell culture is exerted by supplementing the mediaof cells expressing the protein of interest with suitable combinationsof arginine, lysine, calcium chloride and niacinamide.

In certain embodiments, control over the amount of acidic speciesproduced by cell culture is exerted by ensuring that the production of aprotein, for example, an antibody, of interest occurs under specificconditions, including specific pH.

In certain embodiments, control over the amount of acidic species ofprotein produced by cell culture is exerted by supplementing the mediaof cells expressing the protein of interest with arginine and lysine andby controlling the pH of the cell culture. In certain embodiments, thepH of the cell culture is adjusted to a pH of about 6.9. In certainembodiments, the pH of the cell culture is adjusted to a lower pH ofabout 6.8.

In certain embodiments, control over the amount of acidic species ofprotein produced by cell culture is exerted by supplementing the mediaof cells expressing the protein of interest with arginine and lysine andby choice of cell culture harvest criteria. In certain embodiments, theharvest criterion is a particular culture day. In certain embodiments,the harvest criterion is based on harvest viability.

In certain embodiments, control over the amount of acidic speciesproduced by cell culture is exerted by supplementing a cell cultureclarified harvest comprising a protein or antibody of interest with oneor more amino acids. In certain embodiments, the one or more amino acidsis arginine, histidine, or combinations thereof.

In certain embodiments, control over the amount of acidic speciesproduced by cell culture is exerted by adjusting the pH of a cellculture clarified harvest comprising a protein or antibody of interest.In certain embodiments, the pH of the cell culture clarified harvest isadjusted to a pH of about 5. In certain embodiments, the pH of the cellculture clarified harvest is adjusted to a pH of about 6.

In certain embodiments, control over the amount of acidic speciesproduced by cell culture is exerted by the use of a continuous orperfusion technology. In certain embodiments, this may be attainedthrough choice of medium exchange rate. In certain, non-limiting,embodiments, maintenance of the medium exchange rates (workingvolumes/day) of a cell culture run between 0 and 20, or between 0.5 and12 or between 1 and 8 or between 1.5 and 6 can be used to achieve thedesired reduction in acidic species. In certain embodiments, the choiceof cell culture methodology that allows for control of acidic speciesheterogeneity can also include, for example, but not by way oflimitation, employment of an intermittent harvest strategy or throughuse of cell retention device technology.

In certain embodiments, the methods of culturing cells expressing aprotein of interest, such as an antibody or antigen-binding portionthereof, reduces the amount of acidic species present in the resultingcomposition. In certain embodiments, the resulting composition issubstantially free of acidic species. In one aspect, the samplecomprises a cell culture harvest wherein the cell culture is employed toproduce specific proteins of the present invention. In a particularaspect, the sample matrix is prepared from a cell line used to produceanti-TNF-α antibodies.

The purity of the proteins of interest in the resultant sample productcan be analyzed using methods well known to those skilled in the art,e.g., weak cation exchange chromatography (WCX), capillary isoelectricfocusing (cIEF), size-exclusion chromatography, Porosn™ A HPLC Assay,HCP ELISA, Protein A ELISA, and western blot analysis.

In yet another embodiment, the invention is directed to one or morepharmaceutical compositions comprising an isolated protein, such as anantibody or antigen-binding portion thereof, and an acceptable carrier.In another aspect, the compositions further comprise one or morepharmaceutical agents.

4. BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts the effect of total arginine concentration in adalimumabproducing cell line 2, media 1 on viable cell density (n=2).

FIG. 2 depicts the effect of total arginine concentration in adalimumabproducing cell line 2, media 1 on viability (n=2).

FIG. 3 depicts the effect of total arginine concentration in adalimumabproducing cell line 2, media 1 on harvest titer (n=2).

FIG. 4 depicts the effect of total arginine concentration in adalimumabproducing cell line 2, media 1 on day 10 WCX 10 profile total acidicregions (n=2).

FIG. 5 depicts the effect of total arginine concentration in adalimumabproducing cell line 2, media 1 on day 12 WCX 10 profile total acidicregions (n=2).

FIG. 6 depicts the effect of total arginine concentration in adalimumabproducing cell line 3, media 1 on viable cell density (n=2).

FIG. 7 depicts the effect of total arginine concentration in adalimumabproducing cell line 3, media 1 on viability (n=2).

FIG. 8 depicts the effect of total arginine concentration in adalimumabproducing cell line 3, media 1 on harvest titer (n=2).

FIG. 9 depicts the effect of total arginine concentration in adalimumabproducing cell line 3, media 1 on WCX 10 profile total acidic regions(n=2).

FIG. 10 depicts the effect of total arginine concentration in adalimumabproducing cell line 1, media 1 on WCX 10 profile total acidic regions(n=2).

FIG. 11 depicts the effect of arginine addition to adalimumab producingcell line 1, media 2 on day 11 on WCX-10 profile total acidic regions(n=2).

FIG. 12 depicts the effect of arginine addition to adalimumab producingcell line 2, media 3 on WCX-10 profile total acidic regions (n=2).

FIG. 13 depicts the effect of total arginine concentration in mAB1producing cell line on WCX-10 profile total acidic regions (n=1).

FIG. 14 depicts the effect of total arginine concentration in mAB2producing cell line on WCX-10 profile total acidic regions (n=2)

FIG. 15 depicts the effect of carboxypeptidase digestion of product fromadalimumab producing cell line 3, media 1 experiment on WCX-10 profiletotal acidic regions (n=1).

FIG. 16 depicts the effect of carboxypeptidase digestions of productfrom mAB2 producing cell line on WCX-10 profile total acidic regions(n=2).

FIG. 17 depicts the effect of total lysine concentration in adalimumabproducing cell line 2, media 1 on viable cell density (n=2).

FIG. 18 depicts the effect of total lysine concentration in adalimumabproducing cell line 2, media 1 on viability (n=2).

FIG. 19 depicts the effect of total lysine concentration in adalimumabproducing cell line 2, media 1 on harvest titer (n=2).

FIG. 20 depicts the effect of total lysine concentration in adalimumabproducing cell line 2, media 1 on WCX 10 profile total acidic regions(n=2).

FIG. 21 depicts the effect of total lysine concentration in adalimumabproducing cell line 3, media 1 on viable cell density (n=2).

FIG. 22 depicts the effect of total lysine concentration in adalimumabproducing cell line 3, media 1 on viability (n=2).

FIG. 23 depicts the effect of total lysine concentration in adalimumabproducing cell line 3, media 1 on harvest titer (n=2).

FIG. 24 depicts the effect of total lysine concentration in adalimumabproducing cell line 3, media 1 on WCX 10 profile total acidic regions(n=2).

FIG. 25 depicts the effect of total lysine concentration in adalimumabproducing cell line 1, media 1 on WCX 10 profile total acidic regions(n=2).

FIG. 26 depicts the effect of lysine addition to adalimumab producingcell line 1, media 2 on WCX-10 profile total acidic regions (n=2).

FIG. 27 depicts the effect of lysine addition to adalimumab producingcell line 2, media 3 on WCX-10 profile total acidic regions (n=2).

FIG. 28 depicts the effect of total lysine concentration in mAB1producing cell line on WCX-10 profile total acidic regions (n=1).

FIG. 29 depicts the effect of total lysine concentration in mAB2producing cell line on WCX-10 profile total acidic regions (n=2).

FIG. 30 depicts the effect of carboxypeptidase digestion of product fromcell line 3, media 1 experiment on WCX-10 profile total acidic regions(n=1).

FIG. 31 depicts the effect of carboxypeptidase digestions of productfrom mAB2 to producing cell line on WCX-10 profile total acidic regions(n=2).

FIG. 32 depicts the effect of total histidine concentration inadalimumab producing cell line 2, media 1 on viable cell density (n=2).

FIG. 33 depicts the effect of total histidine concentration inadalimumab producing cell line 2, media 1 on viability (n=2).

FIG. 34 depicts the effect of total histidine concentration inadalimumab producing cell line 2, media 1 on harvest titer (n=2).

FIG. 35 depicts the effect of total histidine concentration inadalimumab producing cell line 2, media 1 on WCX 10 profile total acidicregions (n=2).

FIG. 36 depicts the effect of total histidine concentration inadalimumab producing cell line 3, media 1 on viable cell density (n=2).

FIG. 37 depicts the effect of total histidine concentration inadalimumab producing cell line 3, media 1 on viability (n=2).

FIG. 38 depicts the effect of total histidine concentration inadalimumab producing cell line 3, media 1 on harvest titer (n=2).

FIG. 39 depicts the effect of total histidine concentration inadalimumab producing cell line 3, media 1 on WCX 10 profile total acidicregions (n=2).

FIG. 40 depicts the effect of total histidine concentration inadalimumab producing cell line 1, media 1 on WCX 10 profile total acidicregions (n=2).

FIG. 41 depicts the effect of histidine addition to adalimumab producingcell line 1, media 2 on WCX-10 profile total acidic regions (n=2).

FIG. 42 depicts the effect of histidine addition to adalimumab producingcell line 2, media 3 on WCX-10 profile total acidic regions (n=2).

FIG. 43 depicts the effect of total histidine concentration in mAB1producing cell line on WCX-10 profile total acidic regions (n=1).

FIG. 44 depicts the effect of total histidine concentration in mAB2producing cell line on WCX-10 profile total acidic regions (n=2).

FIG. 45 depicts the effect of carboxypeptidase digestion of product fromcell line 3, media 1 experiment on WCX-10 profile total acidic regions(n=1).

FIG. 46 depicts the effect of carboxypeptidase digestions of productfrom mAB2 producing cell line on WCX-10 profile total acidic regions(n=2).

FIG. 47 depicts the effect of total ornithine concentration inadalimumab producing cell line 2, media 1 on viable cell density (n=2).

FIG. 48 depicts the effect of total ornithine concentration inadalimumab producing cell line 2, media 1 on viability (n=2).

FIG. 49 depicts the effect of total ornithine concentration inadalimumab producing cell line 2, media 1 on harvest titer (n=2).

FIG. 50 depicts the effect of total ornithine concentration inadalimumab producing cell line 2, media 1 on WCX 10 profile total acidicregions.

FIG. 51 depicts the effect of total ornithine concentration inadalimumab producing cell line 3, media 1 on viable cell density (n=2).

FIG. 52 depicts the effect of total ornithine concentration inadalimumab producing cell line 3, media 1 on viability (n=2).

FIG. 53 depicts the effect of total ornithine concentration inadalimumab producing cell line 3, media 1 on harvest titer (n=2).

FIG. 54 depicts the effect of total ornithine concentration inadalimumab producing cell line 3, media 1 on WCX 10 profile total acidicregions (n=2).

FIG. 55 depicts the effect of total ornithine concentration inadalimumab producing cell line 1, media 1 on WCX 10 profile total acidicregions (n=2).

FIG. 56 depicts the effect of ornithine addition to adalimumab producingcell line 1, media 2 on WCX-10 profile total acidic regions (n=2).

FIG. 57 depicts the effect of ornithine addition to adalimumab producingcell line 2, media 3 on WCX-10 profile total acidic regions (n=2).

FIG. 58 depicts the effect of total ornithine concentration in mAB1producing cell line on WCX-10 profile total acidic regions (n=1).

FIG. 59 depicts the effect of total ornithine concentration in mAB2producing cell line on WCX-10 profile total acidic regions (n=2).

FIG. 60 depicts the effect of carboxypeptidase digestion of product fromcell line 3, media 1 experiment on WCX-10 profile total acidic regions(n=1).

FIG. 61 depicts the effect of carboxypeptidase digestions of productfrom mAB2 producing cell line on WCX-10 profile total acidic regions(n=2).

FIG. 62 depicts the effect of multiple amino acid additions toadalimumab producing cell line 2, media 1 on WCX 10 profile total acidicregions (n=2).

FIG. 63 depicts the effect of increased arginine and lysineconcentration in adalimumab producing cell line 1, media 1 on viablecell density (n=3).

FIG. 64 depicts the effect of increased arginine and lysineconcentration in adalimumab producing cell line 3, media 1 on viability(n=3).

FIG. 65 depicts the effect of increased arginine and lysineconcentration in adalimumab producing cell line 3, media 1 on culturetiter (n=3).

FIG. 66 depicts the effect of increased arginine and lysineconcentration in adalimumab producing cell line 1, media 1 on WCX 10profile total acidic regions (n=2).

FIG. 67 depicts the effect of arginine, lysine and pH modulation toadalimumab producing cell line 1, media 1 on viable cell density (n=2).

FIG. 68 depicts the effect of arginine, lysine and pH modulation toadalimumab producing cell line 3, media 1 on viability (n=2).

FIG. 69 depicts the effect of arginine, lysine and pH modulation toadalimumab producing cell line 3, media 1 on culture titer (n=2).

FIG. 70 depicts the effect of arginine, lysine and pH modulation toadalimumab producing cell line 1, media 1 on WCX 10 profile total acidicregions (n=2).

FIG. 71 depicts the effect of total calcium concentration in adalimumabproducing cell line 2, media 1 on viable cell density (n=2).

FIG. 72 depicts the effect of total calcium concentration in adalimumabproducing cell line 2, media 1 on viability (n=2).

FIG. 73 depicts the effect of total calcium concentration in adalimumabproducing cell line 2, media 1 on harvest titer (n=2).

FIG. 74 depicts the effect of total calcium concentration in adalimumabproducing cell line 2, media 1 on WCX 10 profile total acidic regions(n=2).

FIG. 75 depicts the effect of total calcium concentration in adalimumabproducing cell line 3, media 1 on viable cell density (n=2).

FIG. 76 depicts the effect of total calcium concentration in adalimumabproducing cell line 3, media 1 on viability (n=2).

FIG. 77 depicts the effect of total calcium concentration in adalimumabproducing cell line 3, media 1 on harvest titer (n=2)

FIG. 78 depicts the effect of total calcium concentration in adalimumabproducing cell line 3, media 1 on WCX 10 profile total acidic regions(n=2).

FIG. 79 depicts the effect of total calcium concentration in adalimumabproducing cell line 1, media 1 on WCX 10 profile total acidic regions(n=2).

FIG. 80 depicts the effect of calcium addition to adalimumab producingcell line 1, media 2 on WCX-10 profile total acidic regions (n=2).

FIG. 81 depicts the effect of calcium addition to adalimumab producingcell line 2, media 3 on WCX-10 profile total acidic regions (n=2).

FIG. 82 depicts the effect of total calcium concentration in mAB1producing cell line on WCX-10 profile total acidic regions (n=2).

FIG. 83 depicts the effect of total calcium concentration in mAB2producing cell line on WCX-10 profile total acidic regions (n=2).

FIG. 84 depicts the effect of multiple amino acid additions to cell line1, media 1 on WCX 10 profile total acidic regions a) overall predictionplot, b) prediction plots for each additive (n=2).

FIG. 85 depicts the effect of niacinamide addition to adalimumabproducing cell line 1, media 1 on viable cell density (n=2).

FIG. 86 depicts the effect of niacinamide addition to adalimumabproducing cell line 1, media 1 on viability (n=2).

FIG. 87 depicts the effect of niacinamide addition to adalimumabproducing cell line 1, media 1 on harvest titer (n=2).

FIG. 88 depicts the effect of niacinamide addition to adalimumabproducing cell line 1, media 1 on Day 11 WCX 10 profile total acidicregions (n=2).

FIG. 89 depicts the effect of niacinamide addition to adalimumabproducing cell line 1, media 1 on Day 12 WCX-10 profile total acidicregions (n=2).

FIG. 90 depicts the effect of niacinamide addition to mAB2 producingcell line, media 1 on viable cell density (n=2).

FIG. 91 depicts the effect of niacinamide addition to mAB2 producingcell line, media 1 on viability (n=2).

FIG. 92 depicts the effect of niacinamide addition to mAB2 producingcell line, media 1 on harvest titer (n=2).

FIG. 93 depicts the effect of niacinamide addition to mAB2 producingcell line, media 1 on WCX 10 profile total acidic regions (n=2).

FIG. 94 depicts the effect of pH modulation of adalimumab producing cellline 1, media 1 on viable cell density (n=2).

FIG. 95 depicts the effect of pH modulation adalimumab producing cellline 1, media 1 on viability (n=2).

FIG. 96 depicts the effect of pH modulation of adalimumab producing cellline 1, media 1 on harvest titer (n=2).

FIG. 97 depicts the effect of pH modulation of adalimumab producing cellline 1, media 1 on WCX 10 profile total acidic regions (n=2).

FIG. 98 depicts the effect of pH modulation of adalimumab producing cellline 1, media 2 on viable cell density (n=2).

FIG. 99 depicts the effect of pH modulation addition of adalimumabproducing adalimumab producing cell line 1, media 2 on viability (n=2).

FIG. 100 depicts the effect of pH modulation of adalimumab producingcell line 1, media 2 on harvest titer (n=2).

FIG. 101 depicts the effect of pH modulation of adalimumab producingcell line 1, media 2 on WCX 10 profile total acidic regions (n=2).

FIG. 102 depicts the effect of pH modulation of adalimumab producingcell line 3, media 1 on viable cell density (n=2).

FIG. 103 depicts the effect of pH modulation adalimumab producing cellline 3, media 1 on viability (n=2).

FIG. 104 depicts the effect of pH modulation of adalimumab producingcell line 3, media 1 on harvest titer (n=2).

FIG. 105 depicts the effect of pH modulation of adalimumab producingcell line 3, media 1 on WCX 10 profile total acidic regions (n=2).

FIG. 106 depicts an acidification sample preparation scheme.

FIG. 107 depicts an arginine sample preparation scheme.

FIG. 108 depicts a histidine sample preparation scheme.

FIG. 109 depicts a lysine sample preparation scheme.

FIG. 110 depicts a methionine sample preparation scheme.

FIG. 111 depicts an amino acid sample preparation scheme.

FIG. 112 depicts a CDM clarified harvest sample preparation scheme.

FIG. 113 depicts an acid-type pH study sample preparation scheme.

FIG. 114 depicts the effect of low pH treatment with subsequentneutralization on initial acidic variant content.

FIG. 115 depicts the effect of low pH treatment with subsequentneutralization on acidic variant formation rate.

FIG. 116 depicts the effect of sample preparation method on initialacidic variant content.

FIG. 117 depicts the effect of sample preparation method on initialacidic variant content.

FIG. 118 depicts the dose dependent effect of arginine on reduction ofacidic variant formation rate.

FIG. 119 depicts the effect of histidine concentration on initial acidicvariant content.

FIG. 120 depicts the effect of histidine concentration on acidic variantformation rate.

FIG. 121 depicts the effect of lysine on initial acid variant content.

FIG. 122 depicts the effect of lysine on acidic variant formation rate.

FIG. 123 depicts the effect of methionine on initial acid variantcontent.

FIG. 124 depicts the effect of methionine on acidic variant formationrate.

FIG. 125 depicts the effect of amino acids on initial acid variantcontent.

FIG. 126 depicts the effect of amino acids on acidic variant formationrate.

FIG. 127 depicts the effect of alternative additives on initial acidvariant content.

FIG. 128 depicts the effect of alternative additives on acidic variantformation rate.

FIG. 129 depicts the effect of low pH/arginine treatment on D2E7 CDMinitial acid variant content.

FIG. 130 depicts the effect of low pH/arginine treatment on D2E7 CDMacidic variant formation rate.

FIG. 131 depicts the effect of low pH/arginine treatment on mAb Bhydrolysate initial acid variant content.

FIG. 132 depicts the effect of low pH/arginine treatment on mAb Bhydrolysate acidic variant formation rate.

FIG. 133 depicts the effect of low pH/arginine treatment on mAb Chydrolysate initial acid variant content.

FIG. 134 depicts the effect of low pH/arginine treatment on mAb Chydrolysate acidic variant formation rate.

FIG. 135 depicts the effect of acid type/pH on acid variant content.

FIG. 136 depicts the effect of acid concentration on acid variantcontent.

FIG. 137 depicts the effect of acid concentration on acid variantcontent.

FIG. 138 depicts the effect of neutralization on acid variant content.

FIG. 139 depicts the effect of neutralization on acid variant content.

FIG. 140 depicts LC/MS peptide mapping analysis of exemplary antibodiesexpressed in the context of the cell culture conditions of the instantinvention, including preparation of specific mass traces for bothmodified and non-modified peptides in order to accurately quantify thetotal amount of MGO modification. Mass spectra are also analyzed for thespecific region of the chromatogram to confirm the peptide identity.

FIG. 141 depicts a chromatogram wherein the total acidic speciesassociated with the expression of Adalimiumab is divided into a firstacidic species region (AR1) and a second acidic species region (AR2).

FIG. 142 depicts the AR Growth at 25° C. of low and high AR containingsamples.

5. DETAILED DESCRIPTION OF THE INVENTION

The instant invention relates to the field of protein production. Inparticular, the instant invention relates to compositions and processesfor controlling the amount of acidic species expressed by host cellswhen used to produce a protein of interest. Certain embodiments of theinvention relate to culturing said cells to express said proteins underconditions that limit the amount of acidic species that are expressed bythe cells. In certain embodiments, the methods described herein employculturing said cells in media supplemented with one or more amino acidsand/or calcium (e.g., as calcium chloride dihydrate) and/or niacinamide.In certain embodiments, the methods described herein employ culturingsaid cells in a culture with appropriate control of process parameters,such as pH. In certain embodiments, methods described herein employculturing cells at a lower process pH. In certain embodiments of theinstant invention, control of acidic species heterogeneity can beattained by the choice of cell culture methodology. In certainembodiments, use of a continuous or perfusion technology may be utilizedto achieve the desired control over acidic species heterogeneity. Incertain embodiments, this may be attained through choice of mediumexchange rate. In certain embodiments, the present invention is directedtoward pharmaceutical compositions comprising one or more proteins, suchas, but not limited to an antibody or antigen-binding portion thereof,purified by a method described herein.

For clarity and not by way of limitation, this detailed description isdivided into the following sub-portions:

(1) Definitions;

(ii) Antibody Generation;

(iii) Protein Production;

(iv) Protein Purification;

(v) Pharmaceutical Compositions

5.1 DEFINITIONS

In order that the present invention may be more readily understood,certain terms are first defined.

As used herein, the terms “acidic species” and “acidic speciesheterogeneity” refer to a characteristic of a population of proteinswherein the population includes a distribution of product-relatedimpurities identifiable by the presence of charge heterogeneities. Forexample, in monoclonal antibody (mAb) preparations, such acidic speciesheterogeneities can be detected by various methods, such as, forexample, WCX-10 HPLC (a weak cation exchange chromatography), or IEF(isoelectric focusing). In certain embodiments, the acidic speciesidentified using such techniques comprise a mixture of product-relatedimpurities containing antibody product fragments (e.g., Fc and Fabfragments), chemical modifications (e.g., methylglyoxal modified species(as described in the U.S. patent application having attorney referenceno. ABV11886USL1), glycated species) and/or post-translationmodifications of the antibody product, such as, deamidated and/orglycoslyated antibodies.

In certain embodiments, the acidic species heterogeneity comprises adifference in the type of acidic species present in the population ofproteins. For example, the population of proteins may comprise more thanone acidic species variant. For example, but not by way of limitation,the total acidic species can be divided based on chromatographicresidence time. FIG. 141 depicts a non-limiting example of such adivision wherein the total acidic species associated with the expressionof Adalimiumab is divided into a first acidic species region (AR1) and asecond acidic species region (AR2). The compositions of particularacidic species regions may differ depending on the particular antibodyof interest, as well as the particular cell culture, purification,and/or chromatographic conditions employed.

In certain embodiments, the heterogeneity of the distribution of acidicspecies comprises a difference in the amount of acidic species in thepopulation of proteins. For example, the population of proteins maycomprise more than one acidic species variant, and each of the variantsmay be present in different amounts.

The term “antibody” includes an immunoglobulin molecule comprised offour polypeptide chains, two heavy (H) chains and two light (L) chainsinter-connected by disulfide bonds. Each heavy chain is comprised of aheavy chain variable region (abbreviated herein as HCVR or VH) and aheavy chain constant region (CH). The heavy chain constant region iscomprised of three domains, CH1, CH2 and CH3. Each light chain iscomprised of a light chain variable region (abbreviated herein as LCVRor VL) and a light chain constant region. The light chain constantregion is comprised of one domain, CL. The VH and VL regions can befurther subdivided into regions of hypervariability, termedcomplementarity determining regions (CDRs), interspersed with regionsthat are more conserved, termed framework regions (FR). Each VH and VLis composed of three CDRs and four FRs, arranged from amino-terminus tocarboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3,CDR3, FR4.

The term “antigen-binding portion” of an antibody (or “antibodyportion”) includes fragments of an antibody that retain the ability tospecifically bind to an antigen (e.g., in the case of Adalimumab,hTNFα). It has been shown that the antigen-binding function of anantibody can be performed by fragments of a full-length antibody.Examples of binding fragments encompassed within the term“antigen-binding portion” of an antibody include (i) a Fab fragment, amonovalent fragment comprising the VL, VH, CL and CH1 domains; (ii) aF(ab′)2 fragment, a bivalent fragment comprising two Fab fragmentslinked by a disulfide bridge at the hinge region; (iii) a Fd fragmentcomprising the VH and CH1 domains; (iv) a Fv fragment comprising the VLand VH domains of a single arm of an antibody, (v) a dAb fragment (Wardet al., (1989) Nature 341:544-546, the entire teaching of which isincorporated herein by reference), which comprises a VH domain; and (vi)an isolated complementarity determining region (CDR). Furthermore,although the two domains of the Fv fragment, VL and VH, are coded for byseparate genes, they can be joined, using recombinant methods, by asynthetic linker that enables them to be made as a single protein chainin which the VL and VH regions pair to form monovalent molecules (knownas single chain Fv (scFv); see, e.g., Bird et al. (1988) Science242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci. USA85:5879-5883, the entire teachings of which are incorporated herein byreference). Such single chain antibodies are also intended to beencompassed within the term “antigen-binding portion” of an antibody.Other forms of single chain antibodies, such as diabodies are alsoencompassed. Diabodies are bivalent, bispecific antibodies in which VHand VL domains are expressed on a single polypeptide chain, but using alinker that is too short to allow for pairing between the two domains onthe same chain, thereby forcing the domains to pair with complementarydomains of another chain and creating two antigen binding sites (see,e.g., Holliger, P., et al. (1993) Proc. Natl. Acad. Sci. USA90:6444-6448; Poljak, R. J., et al. (1994) Structure 2:1121-1123, theentire teachings of which are incorporated herein by reference). Stillfurther, an antibody or antigen-binding portion thereof may be part of alarger immunoadhesion molecule, formed by covalent or non-covalentassociation of the antibody or antibody portion with one or more otherproteins or peptides. Examples of such immunoadhesion molecules includeuse of the streptavidin core region to make a tetrameric scFv molecule(Kipriyanov, S. M., et al. (1995) Human Antibodies and Hybridomas6:93-101, the entire teaching of which is incorporated herein byreference) and use of a cysteine residue, a marker peptide and aC-terminal polyhistidine tag to make bivalent and biotinylated scFvmolecules (Kipriyanov, S. M., et al. (1994) Mal. Immunol. 31:1047-1058,the entire teaching of which is incorporated herein by reference).Antibody portions, such as Fab and F(ab′)2 fragments, can be preparedfrom whole antibodies using conventional techniques, such as papain orpepsin digestion, respectively, of whole antibodies. Moreover,antibodies, antibody portions and immunoadhesion molecules can beobtained using standard recombinant DNA techniques, as described herein.In one aspect, the antigen binding portions are complete domains orpairs of complete domains.

The phrase “clarified harvest” refers to a liquid material containing aprotein of interest, for example, an antibody of interest such as amonoclonal or polyclonal antibody of interest, that has been extractedfrom cell culture, for example, a fermentation bioreactor, afterundergoing centrifugation to remove large solid particles and subsequentfiltration to remove finer solid particles and impurities from thematerial.

The term “human antibody” includes antibodies having variable andconstant regions corresponding to human germline immunoglobulinsequences as described by Kabat et al. (See Kabat, et al. (1991)Sequences of proteins of Immunological Interest, Fifth Edition, U.S.Department of Health and Human Services, NIH Publication No. 91-3242).The human antibodies of the invention may include amino acid residuesnot encoded by human germline immunoglobulin sequences (e.g., mutationsintroduced by random or site-specific mutagenesis in vitro or by somaticmutation in vivo), e.g., in the CDRs and in particular CDR3. Themutations can be introduced using the “selective mutagenesis approach.”The human antibody can have at least one position replaced with an aminoacid residue, e.g., an activity enhancing amino acid residue which isnot encoded by the human germline immunoglobulin sequence. The humanantibody can have up to twenty positions replaced with amino acidresidues which are not part of the human germline immunoglobulinsequence. In other embodiments, up to ten, up to five, up to three or upto two positions are replaced. In one embodiment, these replacements arewithin the CDR regions. However, the term “human antibody”, as usedherein, is not intended to include antibodies in which CDR sequencesderived from the germline of another mammalian species, such as a mouse,have been grafted onto human framework sequences.

The phrase “recombinant human antibody” includes human antibodies thatare prepared, expressed, created or isolated by recombinant means, suchas antibodies expressed using a recombinant expression vectortransfected into a host cell, antibodies isolated from a recombinant,combinatorial human antibody library, antibodies isolated from an animal(e.g., a mouse) that is transgenic for human immunoglobulin genes (see,e.g., Taylor, L. D., et al. (1992) Nucl. Acids Res. 20:6287-6295, theentire teaching of which is incorporated herein by reference) orantibodies prepared, expressed, created or isolated by any other meansthat involves splicing of human immunoglobulin gene sequences to otherDNA sequences. Such recombinant human antibodies have variable andconstant regions derived from human germline immunoglobulin sequences(see, Kabat, E. A., et al. (1991) Sequences of Proteins of ImmunologicalInterest, Fifth Edition, U.S. Department of Health and Human Services,NIH Publication No. 91-3242). In certain embodiments, however, suchrecombinant human antibodies are subjected to in vitro mutagenesis (or,when an animal transgenic for human Ig sequences is used, in vivosomatic mutagenesis) and thus the amino acid sequences of the VH and VLregions of the recombinant antibodies are sequences that, while derivedfrom and related to human germline VH and VL sequences, may notnaturally exist within the human antibody germline repertoire in vivo.In certain embodiments, however, such recombinant antibodies are theresult of selective mutagenesis approach or back-mutation or both.

An “isolated antibody” includes an antibody that is substantially freeof other antibodies having different antigenic specificities (e.g., anisolated antibody that specifically binds hTNFα is substantially free ofantibodies that specifically bind antigens other than hTNFα). Anisolated antibody that specifically binds hTNFα may bind TNFα moleculesfrom other species. Moreover, an isolated antibody may be substantiallyfree of other cellular material and/or chemicals. A suitable anti-TNFαantibody is Adalimumab (Abbott Laboratories).

As used herein, the term “adalimumab”, also known by its trade nameHumira® (AbbVie) refers to a human IgG antibody that binds the humanform of tumor necrosis factor alpha. In general, the heavy chainconstant domain 2 (CH2) of the adalimumab IgG-Fc region is glycosylatedthrough covalent attachment of oligosaccharide at asparagine 297(Asn-297). Weak cation-exchange chromatography (WCX) analysis of theantibody has shown that it has three main charged-variants (i.e. Lys 0,Lys 1, and Lys 2). These variants, or charged isomers, are the result ofincomplete posttranslational cleavage of the C-terminal lysine residues.In addition to the lysine variants, the WCX-10 analysis measures thepresence acidic species. These acidic regions (i.e., acidic species) areclassified as product-related impurities that are relatively acidic whencompared to the lysine variants and elute before the Lys 0 peak in thechromatogram (FIG. 1).

The term “activity” includes activities such as the bindingspecificity/affinity of an antibody for an antigen, and includesactivities such as the binding specificity/affinity of an anti-TNFαantibody for its antigen, e.g., an anti-TNFα antibody that binds to aTNFα antigen and/or the neutralizing potency of an antibody, e.g., ananti-TNFα antibody whose binding to hTNFα inhibits the biologicalactivity of hTNFα.

The phrase “nucleic acid molecule” includes DNA molecules and RNAmolecules. A nucleic acid molecule may be single-stranded ordouble-stranded, but in one aspect is double-stranded DNA.

The phrase “isolated nucleic acid molecule,” as used herein in referenceto nucleic acids encoding antibodies or antibody portions (e.g., VH, VL,CDR3), e.g. those that bind hTNFα, and includes a nucleic acid moleculein which the nucleotide sequences encoding the antibody or antibodyportion are free of other nucleotide sequences encoding antibodies orantibody portions that bind antigens other than hTNFα, which othersequences may naturally flank the nucleic acid in human genomic DNA.Thus, e.g., an isolated nucleic acid of the invention encoding a VHregion of an anti-TNFα antibody contains no other sequences encodingother VH regions that bind antigens other than, for example, hTNFα. Thephrase “isolated nucleic acid molecule” is also intended to includesequences encoding bivalent, bispecific antibodies, such as diabodies inwhich VH and VL regions contain no other sequences other than thesequences of the diabody.

The phrase “recombinant host cell” (or simply “host cell”) includes acell into which a recombinant expression vector has been introduced. Itshould be understood that such terms are intended to refer not only tothe particular subject cell but to the progeny of such a cell. Becausecertain modifications may occur in succeeding generations due to eithermutation or environmental influences, such progeny may not, in fact, beidentical to the parent cell, but are still included within the scope ofthe term “host cell” as used herein.

As used herein, the term “recombinant protein” refers to a proteinproduced as the result of the transcription and translation of a genecarried on a recombinant expression vector that has been introduced intoa host cell. In certain embodiments the recombinant protein is anantibody, preferably a chimeric, humanized, or fully human antibody. Incertain embodiments the recombinant protein is an antibody of an isotypeselected from group consisting of: IgG (e.g., IgG1, IgG2, IgG3, IgG4),IgM, IgA1, IgA2, IgD, or IgE. In certain embodiments the antibodymolecule is a full-length antibody (e.g., an IgG1 or IgG4immunoglobulin) or alternatively the antibody can be a fragment (e.g.,an Fc fragment or a Fab fragment).

As used herein, the term “cell culture” refers to methods and techniquesemployed to generate and maintain a population of host cells capable ofproducing a recombinant protein of interest, as well as the methods andtechniques for optimizing the production and collection of the proteinof interest. For example, once an expression vector has beenincorporated into an appropriate host, the host can be maintained underconditions suitable for high level expression of the relevant nucleotidecoding sequences, and the collection and purification of the desiredrecombinant protein. Mammalian cells are preferred for expression andproduction of the recombinant protein of the present invention, howeverother eukaryotic cell types can also be employed in the context of theinstant invention. See, e.g., Winnacker, From Genes to Clones, VCHPublishers, N.Y., N.Y. (1987), Suitable mammalian host cells forexpressing recombinant proteins according to the invention includeChinese Hamster Ovary (CHO cells) (including dhfr-CHO cells, describedin Urlaub and Chasin, (1980) PNAS USA 77:4216-4220, used with a DHFRselectable marker, e.g., as described in Kaufman and Sharp (1982) Mol.Biol. 159:601-621, the entire teachings of which are incorporated hereinby reference), NS0 myeloma cells, COS cells and SP2 cells. Otherexamples of useful mammalian host cell lines are monkey kidney CV1 linetransformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line(293 or 293 cells subcloned for growth in suspension culture, Graham etal., J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCCCCL 10); Chinese hamster ovary cells/−DHFR(CHO, Urlaub et al., Proc.Natl. Acad. Sci. USA 77:4216 (1980)); mouse sertoli cells (TM4, Mather,Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (CV1 ATCC CCL 70);African green monkey kidney cells (VERO-76, ATCC CRL-1587); humancervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK,ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); humanlung cells (W138, ATCC CCL 75); human liver cells (Hep G2, FIB 8065);mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al.,Annals N.Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and ahuman hepatoma line (Hep G2), the entire teachings of which areincorporated herein by reference.

When using the cell culture techniques of the instant invention, theprotein of interest can be produced intracellularly, in the periplasmicspace, or directly secreted into the medium. In embodiments where theprotein of interest is produced intracellularly, the particulate debris,either host cells or lysed cells (e.g., resulting from homogenization),can be removed by a variety of means, including but not limited to, bycentrifugation or ultrafiltration. Where the protein of interest issecreted into the medium, supernatants from such expression systems canbe first concentrated using a commercially available proteinconcentration filter, e.g., an Amicon™ or Millipore Pellicon™ultrafiltration unit, which can then be subjected to one or moreadditional purification techniques, including but not limited toaffinity chromatography, including protein A affinity chromatography,ion exchange chromatography, such as anion or cation exchangechromatography, and hydrophobic interaction chromatography.

As used herein the term “on-line” refers to processes that areaccomplished in the context of an on-going cell culture run. Forexample, the administration of a particular nutrient or changes intemperature, pH, or dissolved oxygen level occur on-line when suchadministrations or changes are implemented in an existing cell culturerun. Similarly, measurements of certain data are considered on-line ifthat data is being collected in the context of a particular cell culturerun. For example, on-line gas analysis refers to the measurement ofgases introduced into or released from a particular cell culture run. Incontrast, the term “off-line”, as used herein, refers to actions takenoutside the context of a particular cell culture run. For example, theproduction of cell culture media comprising specific concentrations ofparticular components is an example of an off-line activity.

The term “modifying”, as used herein, is intended to refer to changingone or more amino acids in the antibodies or antigen-binding portionsthereof. The change can be produced by adding, substituting or deletingan amino acid at one or more positions. The change can be produced usingknown techniques, such as PCR mutagenesis.

The term “about”, as used herein, is intended to refer to ranges ofapproximately 10-20% greater than or less than the referenced value. Incertain circumstances, one of skill in the art will recognize that, dueto the nature of the referenced value, the term “about” can mean more orless than a 10-20% deviation from that value.

The term “control”, as used herein, is intended to refer to bothlimitation as well as to modulation. For example, in certainembodiments, the instant invention provides methods for controllingdiversity that decrease the diversity of certain characteristics ofprotein populations, including, but not limited to, the presence ofacidic species. Such decreases in diversity can occur by: (1) promotionof a desired characteristic; (2) inhibition of an unwantedcharacteristic; or (3) a combination of the foregoing. As used herein,the term “control” also embraces contexts where heterogeneity ismodulated, i.e., shifted, from one diverse population to a secondpopulation of equal, or even greater diversity, where the secondpopulation exhibits a distinct profile of the characteristic ofinterest.

5.2 ANTIBODY GENERATION

The term “antibody” as used in this section refers to an intact antibodyor an antigen binding fragment thereof.

The antibodies of the present disclosure can be generated by a varietyof techniques, including immunization of an animal with the antigen ofinterest followed by conventional monoclonal antibody methodologiese.g., the standard somatic cell hybridization technique of Kohler andMilstein (1975) Nature 256: 495. Although somatic cell hybridizationprocedures are preferred, in principle, other techniques for producingmonoclonal antibody can be employed e.g., viral or oncogenictransformation of B lymphocytes.

One preferred animal system for preparing hybridomas is the murinesystem. Hybridoma production is a very well-established procedure.Immunization protocols and techniques for isolation of immunizedsplenocytes for fusion are known in the art. Fusion partners (e.g.,murine myeloma cells) and fusion procedures are also known.

An antibody preferably can be a human, a chimeric, or a humanizedantibody. Chimeric or humanized antibodies of the present disclosure canbe prepared based on the sequence of a non-human monoclonal antibodyprepared as described above. DNA encoding the heavy and light chainimmunoglobulins can be obtained from the non-human hybridoma of interestand engineered to contain non-murine (e.g., human) immunoglobulinsequences using standard molecular biology techniques. For example, tocreate a chimeric antibody, murine variable regions can be linked tohuman constant regions using methods known in the art (see e.g., U.S.Pat. No. 4,816,567 to Cabilly et al.). To create a humanized antibody,murine CDR regions can be inserted into a human framework using methodsknown in the art (see e.g., U.S. Pat. No. 5,225,539 to Winter, and U.S.Pat. Nos. 5,530,101; 5,585,089; 5,693,762 and 6,180,370 to Queen etal.).

In one non-limiting embodiment, the antibodies of this disclosure arehuman monoclonal antibodies. Such human monoclonal antibodies can begenerated using transgenic or transchromosomic mice carrying parts ofthe human immune system rather than the mouse system.

These transgenic and transchromosomic mice include mice referred toherein as the HuMAb Mouse® (Medarex, Inc.), KM Mouse® (Medarex, Inc.),and XenoMouse® (Amgen).

Moreover, alternative transchromosomic animal systems expressing humanimmunoglobulin genes are available in the art and can be used to raiseantibodies of the disclosure. For example, mice carrying both a humanheavy chain transchromosome and a human light chain transchromosome,referred to as “TC mice” can be used; such mice are described inTomizuka et al. (2000) Proc. Natl. Acad. Sci. USA 97:722-727.Furthermore, cows carrying human heavy and light chain transchromosomeshave been described in the art (e.g., Kuroiwa et al. (2002) NatureBiotechnology 20:889-894 and PCT application No. WO 2002/092812) and canbe used to raise antibodies of this disclosure.

Recombinant human antibodies of the invention can be isolated byscreening of a recombinant combinatorial antibody library, e.g., a scFvphage display library, prepared using human VL and VH cDNAs preparedfrom mRNA derived from human lymphocytes. Methodologies for preparingand screening such libraries are known in the art. In addition tocommercially available kits for generating phage display libraries(e.g., the Pharmacia Recombinant Phage Antibody System, catalog no.27-9400-01; and the Stratagene SurfZAP™ phage display kit, catalog no.240612, the entire teachings of which are incorporated herein), examplesof methods and reagents particularly amenable for use in generating andscreening antibody display libraries can be found in, e.g., Ladner etal. U.S. Pat. No. 5,223,409; Kang et al. PCT Publication No. WO92/18619; Dower et al. PCT Publication No. WO 91/17271; Winter et al.PCT Publication No. WO 92/20791; Markland et al. PCT Publication No. WO92/15679; Breitling et al. PCT Publication No. WO 93/01288; McCaffertyet al. PCT Publication No. WO 92/01047; Garrard et al. PCT PublicationNo. WO 92/09690; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay etal. (1992) Hum Antibody Hybridomas 3:81-85; Huse et al. (1989) Science246:1275-1281; McCafferty et al., Nature (1990) 348:552-554; Griffithset al. (1993) EMBO J. 12:725-734; Hawkins et al. (1992) J Mol Biol226:889-896; Clackson et al. (1991) Nature 352:624-628; Gram et al.(1992) PNAS 89:3576-3580; Garrard et al. (1991) Bio/Technology9:1373-1377; Hoogenboom et al. (1991) Nuc Acid Res 19:4133-4137; andBarbas et al. (1991) PNAS 88:7978-7982; the entire teachings of whichare incorporated herein.

Human monoclonal antibodies of this disclosure can also be preparedusing SCID mice into which human immune cells have been reconstitutedsuch that a human antibody response can be generated upon immunization.Such mice are described in, for example, U.S. Pat. Nos. 5,476,996 and5,698,767 to Wilson et al.

In certain embodiments, the methods of the invention include anti-TNFαantibodies and antibody portions, anti-TNFα-related antibodies andantibody portions, and human antibodies and antibody portions withequivalent properties to anti-TNFα, such as high affinity binding tohTNFα with low dissociation kinetics and high neutralizing capacity. Inone aspect, the invention provides treatment with an isolated humanantibody, or an antigen-binding portion thereof, that dissociates fromhTNFα with a Kd of about 1×10⁻⁸ M or less and a Koff rate constant of1×10⁻³ s⁻¹ or less, both determined by surface plasmon resonance. Inspecific non-limiting embodiments, an anti-TNFα antibody purifiedaccording to the invention competitively inhibits binding of Adalimumabto TNFα under physiological conditions.

Antibodies or fragments thereof, can be altered wherein the constantregion of the antibody is modified to reduce at least one constantregion-mediated biological effector function relative to an unmodifiedantibody. To modify an antibody of the invention such that it exhibitsreduced binding to the Fc receptor, the immunoglobulin constant regionsegment of the antibody can be mutated at particular regions necessaryfor Fc receptor (FcR) interactions (see, e.g., Canfield and Morrison(1991) J. Exp. Med. 173:1483-1491; and Lund et al. (1991) J. of Immunol.147:2657-2662, the entire teachings of which are incorporated herein).Reduction in FcR binding ability of the antibody may also reduce othereffector functions which rely on FcR interactions, such as opsonizationand phagocytosis and antigen-dependent cellular cytotoxicity.

5.3 PROTEIN PRODUCTION

To express a protein of the invention, such as an antibody orantigen-binding fragment thereof, DNAs encoding the protein, such asDNAs encoding partial or full-length light and heavy chains in the caseof antibodies, are inserted into one or more expression vector such thatthe genes are operatively linked to transcriptional and translationalcontrol sequences. (See, e.g., U.S. Pat. No. 6,914,128, the entireteaching of which is incorporated herein by reference.) In this context,the term “operatively linked” is intended to mean that a gene encodingthe protein of interest is ligated into a vector such thattranscriptional and translational control sequences within the vectorserve their intended function of regulating the transcription andtranslation of the gene. The expression vector and expression controlsequences are chosen to be compatible with the expression host cellused. In certain embodiments, the protein of interest will comprisingmultiple polypeptides, such as the heavy and light chains of anantibody. Thus, in certain embodiments, genes encoding multiplepolypeptides, such as antibody light chain genes and antibody heavychain genes, can be inserted into a separate vector or, more typically,the genes are inserted into the same expression vector. Genes areinserted into expression vectors by standard methods (e.g., ligation ofcomplementary restriction sites on the gene fragment and vector, orblunt end ligation if no restriction sites are present). Prior toinsertion of the gene or genes, the expression vector may already carryadditional polypeptide sequences, such as, but no limited to, antibodyconstant region sequences. For example, one approach to converting theanti-TNFα antibody or anti-TNFα antibody-related VH and VL sequences tofull-length antibody genes is to insert them into expression vectorsalready encoding heavy chain constant and light chain constant regions,respectively, such that the VH segment is operatively linked to the CHsegment(s) within the vector and the VL segment is operatively linked tothe CL segment within the vector. Additionally or alternatively, therecombinant expression vector can encode a signal peptide thatfacilitates secretion of the protein from a host cell. The gene can becloned into the vector such that the signal peptide is linked in-frameto the amino terminus of the gene. The signal peptide can be animmunoglobulin signal peptide or a heterologous signal peptide (i.e., asignal peptide from a non-immunoglobulin protein).

In addition to protein coding genes, a recombinant expression vector ofthe invention can carry one or more regulatory sequence that controlsthe expression of the protein coding genes in a host cell. The term“regulatory sequence” is intended to include promoters, enhancers andother expression control elements (e.g., polyadenylation signals) thatcontrol the transcription or translation of the protein coding genes.Such regulatory sequences are described, e.g., in Goeddel; GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990), the entire teaching of which is incorporatedherein by reference. It will be appreciated by those skilled in the artthat the design of the expression vector, including the selection ofregulatory sequences may depend on such factors as the choice of thehost cell to be transformed, the level of expression of protein desired,etc. Suitable regulatory sequences for mammalian host cell expressioninclude viral elements that direct high levels of protein expression inmammalian cells, such as promoters and/or enhancers derived fromcytomegalovirus (CMV) (such as the CMV promoter/enhancer), Simian Virus40 (SV40) (such as the SV40 promoter/enhancer), adenovirus, (e.g., theadenovirus major late promoter (AdMLP)) and polyoma. For furtherdescription of viral regulatory elements, and sequences thereof, see,e.g., U.S. Pat. No. 5,168,062 by Stinski, U.S. Pat. No. 4,510,245 byBell et al. and U.S. Pat. No. 4,968,615 by Schaffner et al., the entireteachings of which are incorporated herein by reference.

In addition to the protein coding genes and regulatory sequences, arecombinant expression vector of the invention may carry one or moreadditional sequences, such as a sequence that regulates replication ofthe vector in host cells (e.g., origins of replication) and/or aselectable marker gene. The selectable marker gene facilitates selectionof host cells into which the vector has been introduced (see e.g., U.S.Pat. Nos. 4,399,216, 4,634,665 and 5,179,017, all by Axel et al., theentire teachings of which are incorporated herein by reference). Forexample, typically the selectable marker gene confers resistance todrugs, such as G418, hygromycin or methotrexate, on a host cell intowhich the vector has been introduced. Suitable selectable marker genesinclude the dihydrofolate reductase (DHFR) gene (for use in dhfr-hostcells with methotrexate selection/amplification) and the neo gene (forG418 selection).

An antibody, or antibody portion, of the invention can be prepared byrecombinant expression of immunoglobulin light and heavy chain genes ina host cell. To express an antibody recombinantly, a host cell istransfected with one or more recombinant expression vectors carrying DNAfragments encoding the immunoglobulin light and heavy chains of theantibody such that the light and heavy chains are expressed in the hostcell and secreted into the medium in which the host cells are cultured,from which medium the antibodies can be recovered. Standard recombinantDNA methodologies are used to obtain antibody heavy and light chaingenes, incorporate these genes into recombinant expression vectors andintroduce the vectors into host cells, such as those described inSambrook, Fritsch and Maniatis (eds), Molecular Cloning; A LaboratoryManual, Second Edition, Cold Spring Harbor, N.Y., (1989), Ausubel et al.(eds.) Current Protocols in Molecular Biology, Greene PublishingAssociates, (1989) and in U.S. Pat. Nos. 4,816,397 & 6,914,128, theentire teachings of which are incorporated herein.

For expression of protein, for example, the light and heavy chains of anantibody, the expression vector(s) encoding the protein is (are)transfected into a host cell by standard techniques. The various formsof the term “transfection” are intended to encompass a wide variety oftechniques commonly used for the introduction of exogenous DNA into aprokaryotic or eukaryotic host cell, e.g., electroporation,calcium-phosphate precipitation, DEAE-dextran transfection and the like.Although it is theoretically possible to express the proteins of theinvention in either prokaryotic or eukaryotic host cells, expression ofantibodies in eukaryotic cells, such as mammalian host cells, issuitable because such eukaryotic cells, and in particular mammaliancells, are more likely than prokaryotic cells to assemble and secrete aproperly folded and immunologically active protein. Prokaryoticexpression of protein genes has been reported to be ineffective forproduction of high yields of active protein (Boss and Wood (1985)Immunology Today 6:12-13, the entire teaching of which is incorporatedherein by reference).

Suitable host cells for cloning or expressing the DNA in the vectorsherein are the prokaryote, yeast, or higher eukaryote cells describedabove. Suitable prokaryotes for this purpose include eubacteria, such asGram-negative or Gram-positive organisms, e.g., Enterobacteriaceae suchas Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella,Proteus, Salmonella, e.g., Salmonella typhimurium, Serratia, e.g.,Serratia marcescans, and Shigella, as well as Bacilli such as B.subtilis and B. lichenifonnis (e.g., B. licheniformis 41P disclosed inDD 266,710 published Apr. 12, 1989), Pseudomonas such as P. aeruginosa,and Streptomyces. One suitable E. coli cloning host is E. coli 294 (ATCC31,446), although other strains such as E. coli B, E. cob X1776 (ATCC31,537), and E. coli W3110 (ATCC 27,325) are suitable. These examplesare illustrative rather than limiting.

In addition to prokaryotes, eukaryotic microbes such as filamentousfungi or yeast are suitable cloning or expression hosts for polypeptideencoding vectors. Saccharomyces cerevisiae, or common baker's yeast, isthe most commonly used among lower eukaryotic host microorganisms.However, a number of other genera, species, and strains are commonlyavailable and useful herein, such as Schizosaccharomyces pombe;Kluyveromyces hosts such as, e.g., K. lactis, K. fragilis (ATCC 12,424),K. bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii(ATCC 56,500), K. drosophilarum (ATCC 36,906), K. thermotolerans, and K.marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070); Candida;Trichoderma reesia (EP 244,234); Neurospora crassa; Schwanniomyces suchas Schwanniomyces occidentalis; and filamentous fungi such as, e.g.,Neurospora, Penicillium, Tolypocladium, and Aspergillus hosts such as A.nidulans and A. niger.

Suitable host cells for the expression of glycosylated proteins, forexample, glycosylated antibodies, are derived from multicellularorganisms. Examples of invertebrate cells include plant and insectcells. Numerous baculoviral strains and variants and correspondingpermissive insect host cells from hosts such as Spodoptera frugiperda(caterpillar), Aedes aegypti (mosquito), Aedes albopictus (mosquito),Drosophila melanogaster (fruitfly), and Bombyx mori have beenidentified. A variety of viral strains for transfection are publiclyavailable, e.g., the L-1 variant of Autographa californica NPV and theBm-5 strain of Bombyx mori NPV, and such viruses may be used as thevirus herein according to the present invention, particularly fortransfection of Spodoptera frugiperda cells. Plant cell cultures ofcotton, corn, potato, soybean, petunia, tomato, and tobacco can also beutilized as hosts.

Suitable mammalian host cells for expressing the recombinant proteins ofthe invention include Chinese Hamster Ovary (CHO cells) (includingdhfr-CHO cells, described in Urlaub and Chasin, (1980) PNAS USA77:4216-4220, used with a DHFR selectable marker, e.g., as described inKaufman and Sharp (1982) Mol. Biol. 159:601-621, the entire teachings ofwhich are incorporated herein by reference), NS0 myeloma cells, COScells and SP2 cells. When recombinant expression vectors encodingprotein genes are introduced into mammalian host cells, the antibodiesare produced by culturing the host cells for a period of time sufficientto allow for expression of the antibody in the host cells or secretionof the antibody into the culture medium in which the host cells aregrown. Other examples of useful mammalian host cell lines are monkeykidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); humanembryonic kidney line (293 or 293 cells subcloned for growth insuspension culture, Graham et al., J. Gen Virol. 36:59 (1977)); babyhamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovarycells/−DHFR(CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216(1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251(1980)); monkey kidney cells (CV1 ATCC CCL 70); African green monkeykidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells(HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo ratliver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT060562, ATCC CCL51); TRI cells (Mather et al., Annals N.Y, Acad. Sri.383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line(Hep G2), the entire teachings of which are incorporated herein byreference.

Host cells are transformed with the above-described expression orcloning vectors for protein production and cultured in conventionalnutrient media modified as appropriate for inducing promoters, selectingtransformants, or amplifying the genes encoding the desired sequences.

The host cells used to produce a protein may be cultured in a variety ofmedia. Commercially available media such as Ham's F10™ (Sigma), MinimalEssential Medium™ (MEM), (Sigma), RPMI-1640 (Sigma), and Dulbecco'sModified Eagle's Medium™ (DMEM), (Sigma) are suitable for culturing thehost cells. In addition, any of the media described in Ham et al., Meth.Enz. 58:44 (1979), Barnes et al., Anal. Biochem. 102:255 (1980), U.S.Pat. Nos. 4,767,704; 4,657,866; 4,927,762; 4,560,655; or 5,122,469; WO90/03430; WO 87/00195; or U.S. Pat. No. Re. 30,985 may be used asculture media for the host cells, the entire teachings of which areincorporated herein by reference. Any of these media may be supplementedas necessary with hormones and/or other growth factors (such as insulin,transferrin, or epidermal growth factor), salts (such as sodiumchloride, calcium, magnesium, and phosphate), buffers (such as HEPES),nucleotides (such as adenosine and thymidine), antibiotics (such asgentamycin drug), trace elements (defined as inorganic compounds usuallypresent at final concentrations in the micromolar range), and glucose oran equivalent energy source. Any other necessary supplements may also beincluded at appropriate concentrations that would be known to thoseskilled in the art. The culture conditions, such as temperature, pH, andthe like, are those previously used with the host cell selected forexpression, and will be apparent to the ordinarily skilled artisan.

Host cells can also be used to produce portions of intact proteins, farexample, antibodies, including Fab fragments or scFv molecules. It isunderstood that variations on the above procedure are within the scopeof the present invention. For example, in certain embodiments it may bedesirable to transfect a host cell with DNA encoding either the lightchain or the heavy chain (but not both) of an antibody. Recombinant DNAtechnology may also be used to remove some or all of the DNA encodingeither or both of the light and heavy chains that is not necessary forbinding to an antigen. The molecules expressed from such truncated DNAmolecules are also encompassed by the antibodies of the invention. Inaddition, bifunctional antibodies may be produced in which one heavy andone light chain are an antibody of the invention and the other heavy andlight chain are specific for an antigen other than the target antibody,depending on the specificity of the antibody of the invention, bycrosslinking an antibody of the invention to a second antibody bystandard chemical crosslinking methods.

In a suitable system for recombinant expression of a protein, forexample, an antibody, or antigen-binding portion thereof, a recombinantexpression vector encoding the protein, for example, both an antibodyheavy chain and an antibody light chain, is introduced into dhfr-CHOcells by calcium phosphate-mediated transfection. Within the recombinantexpression vector, the protein gene(s) are each operatively linked toCMV enhancer/AdMLP promoter regulatory elements to drive high levels oftranscription of the gene(s). The recombinant expression vector alsocarries a DHFR gene, which allows for selection of CHO cells that havebeen transfected with the vector using methotrexateselection/amplification. The selected transformant host cells arecultured to allow for expression of the protein, for example, theantibody heavy and light chains, and intact protein, for example, anantibody, is recovered from the culture medium. Standard molecularbiology techniques are used to prepare the recombinant expressionvector, transfect the host cells, select for transformants, culture thehost cells and recover the protein from the culture medium.

When using recombinant techniques, the protein, for example, antibodiesor antigen binding fragments thereof, can be produced intracellularly,in the periplasmic space, or directly secreted into the medium. In oneaspect, if the protein is produced intracellularly, as a first step, theparticulate debris, either host cells or lysed cells (e.g., resultingfrom homogenization), can be removed, e.g., by centrifugation orultrafiltration. Where the protein is secreted into the medium,supernatants from such expression systems can be first concentratedusing a commercially available protein concentration filter, e.g., anAmicon™ or Millipore Pellicon™ ultrafiltration unit.

Numerous populations of proteins expressed by host cells, including, butnot limited to, host cells expressing antibodies, such as adalimumab,may comprise a number of acidic species, and are therefore amenable tothe instant invention's methods for control of acidic speciesheterogeneity. For example, weak cation-exchange chromatography (WCX)analysis of adalimumab has shown the presence of acidic regions. Theseacidic species are classified as product-related impurities that arerelatively acidic when compared to the adalimumab protein population.The presence of these acidic species provides an exemplary system toidentify those cell culture conditions that allow for control overacidic species heterogeneity.

5.3.1 Adjusting Amino Acid Concentration to Control Acidic Species

The variation in raw materials used in cell culture, particularly in thecontext of media preparation, can vary product quality significantly.

In certain embodiments of the instant invention, control of acidicspecies heterogeneity can be attained by adjustment of the mediacomposition of the cell culture run. In certain embodiments, suchadjustment will be to increase the amount of one or more amino acids inthe media, while in other embodiments the necessary adjustment toachieve the desired control over acidic species heterogeneity willinvolve a decrease in the amount of one or more amino acids in themedia. Such increases or decreases in the amount of the one or moreamino acids can be of a magnitude of 1%, 5%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%,and ranges within one or more of the preceding, of the original amount.

In certain embodiments, a cell culture media will include one or more ofthe amino acids, or other compositions, described herein as facilitatinga reduction in acidic species. In certain embodiments the amount of theamino acid, or other composition, that is necessary to be supplementedmay be adjusted to account for the amount present in the media prior tosupplementation.

In certain embodiments, the cell culture media is supplemented with oneor more amino acids wherein each of the one or more amino acids issupplemented in an amount of between about 0.025 and 20 g/L, or betweenabout 0.05 and 15 g/L, or between about 0.1 and 14 g/L, or between about0.2 and 13 g/L, or between about 0.25 and 12 g/L, or between about 0.5and 11 g/L, or between about 1 and 10 g/L, or between about 1.5 and 9.5g/L, or between about 2 and 9 g/L, or between about 2.5 and 8.5 g/L, orbetween about 3 and 8 g/L, or between about 3.5 and 7.5 g/L, or betweenabout 4 and 7 g/L, or between about 4.5 and 6.5 g/L, or between about 5and 6 g/L. In certain embodiments, the cell culture media issupplemented with one or more amino acids wherein each of the one ormore amino acids is supplemented in an amount of about 0.25 g/L, orabout 0.5 g/L, or about 1 g/L, or about 2 g/L, or about 4 g/L, or about8 g/L.

In certain embodiments, the cell culture media is supplemented with oneor more amino acids wherein each of the one or more amino acids issupplemented in an amount effective to reduce the amount of acidicspecies heterogeneity in a protein or antibody sample by about 1%, 1.2%,1.5%, 2%, 2.2%, 2.5%, 3%, 3.2%, 3.5%, 4%, 4,2%, 4.5%, 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 100%, and ranges within one or more of the preceding.

In certain embodiments, the one or more amino acids used to supplementthe cell culture media is a basic amino acid. In certain embodiments theone or more amino acids is arginine, lysine, histidine, ornithine, orcertain combinations of arginine or lysine with ornithine or of all fouramino acids. In certain embodiments, the amino acids are provided assingle peptides, as dipeptides, as tripeptides or as longeroligopeptides. In certain embodiments, the di-, tri-, and/oroligopeptides are individually composed of a single amino acid, while inalternative embodiments, the di-, tri-, and/or oligopeptides areindividually composed of two or more particular amino acids. In certainembodiments, the amount of amino acid supplemented to the cell cultureto achieve concentrations of about 0 to about 9 g/l for arginine, about0 to about 11 g/l for lysine, about 0 to about 11 g/l histidine, andabout 0 to about 11 g/l ornithine. Although wider ranges are also withinthe scope of the instant invention, including, but not limited to: about0 to about 30 g/l for arginine, about 0 to about 30 g/l for lysine,about 0 to about 30 g/l histidine, and about 0 to about 30 g/lornithine.

For example, and not by way of limitation, as detailed in Example 6.1,below, when the production medium employed in the example wassupplemented with arginine to achieve a total concentration of 9 g/Larginine, the total amount of acidic species of adalimumab present in acell culture sample after purification was reduced from 19.7% of acontrol sample to 12.2% of the sample purified from the cells culturedwith the arginine supplemented media. Similarly, when the productionmedium employed in the example was supplemented with lysine, orhistidine, or ornithine to achieve total concentrations of 11 g/Llysine, 10 g/L ornithine or 10 g/L histidine, respectively, the totalamount of acidic species of adalimumab present in a cell culture sampleafter purification was reduced by 11.5%, 10.4% and 10.9%, respectively,compared to a control sample.

In certain embodiments, control over the amount of acidic species ofprotein produced by cell culture is exerted by supplementing the mediaof cells expressing the protein of interest medium supplements describedherein such that they can be included in the medium at the start ofculture, or can be added in a fed-batch or in a continuous manner. Thefeed amounts may be calculated to achieve a certain concentration basedon offline or online measurements. The supplements may be added asmultimers, e.g., arg-arg, his-his, arg-his-orn, etc., and/or as chemicalvariants, e.g., of amino acids or analogs of amino acids, salt forms ofamino acids, controlled release of amino acids by immobilizing in gels,etc, and/or in fully or partially dissolved form. The addition of one ormore supplement may be based on measured amount of acidic species. Theresulting media can be used in various cultivation methods including,but not limited to, batch, fed-batch, chemostat and perfusion, and withvarious cell culture equipment including, but not limited to, shakeflasks with or without suitable agitation, spinner flasks, stirredbioreactors, airlift bioreactors, membrane bioreactors, reactors withcells retained on a solid support or immobilized/entrapped as inmicroporous beads, and any other configuration appropriate for optimalgrowth and productivity of the desired cell line. In addition, theharvest criterion for these cultures may be chosen, for example based onchoice of harvest viability or culture duration, to further optimize acertain targeted acidic species profile.

5.3.1 Adjusting CaCl₂ and/or Niacinamide Concentration to Control AcidicSpecies

In certain embodiments, the cell culture media is supplemented withcalcium (e.g., as calcium chloride dihydrate), wherein the calcium issupplemented to achieve a calcium concentration of between about 0.05and 2.5 mM, or between about 0.05 and 1 mM, or between about 0.1 and 0.8mM, or between about 0.15 and 0.7 mM, or between about 0.2 and 0.6 mM,or between about 0.25 and 0.5 mM, or between about 0.3 and 0.4 mM.

In certain embodiments, the cell culture media is supplemented withcalcium (e.g., as calcium chloride dihydrate) wherein the calcium issupplemented in an amount effective to reduce the amount of acidicspecies heterogeneity in a protein or antibody sample by about 1%, 1.2%,1.5%, 2%, 2.2%, 2.5%, 3%, 3.2%, 3.5%, 4%, 4.2%, 4.5%, 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 100%, and ranges within one or more of the preceding.

For example, and not by way of limitation, as detailed in Example 6.3,below, when the production medium employed in the example wassupplemented with calcium (e.g., as calcium chloride dihydrate) at aconcentration of 1.05 mM, the total amount of acidic species ofadalimumab present in a cell culture sample after purification wasreduced from 23.2% of a control sample to 16.5% of the sample purifiedfrom the cells cultured with the calcium supplemented media.

In certain embodiments, the cell culture can be supplemented with acombination of calcium, e.g., CaCl₂, and one or more a basic aminoacids. In certain embodiments the one or more basic amino acids isarginine, lysine, histidine, ornithine, or combinations of arginine orlysine with ornithine or of all four amino acids. In certainembodiments, the amino acids are provided as single peptides, asdipeptides, as tripeptides or as longer oligopeptides. In certainembodiments, the di-, tri-, and/or oligopeptides are individuallycomposed of a single amino acid, while in alternative embodiments, thedi-, tri-, and/or oligopeptides are individually composed of two or moreparticular amino acids. In certain embodiments, the amount of basicamino acid concentrations in combination with calcium in the cellculture is between about 0 to about 9 g/l for arginine, about 0 to about11 g/l for lysine, about 0 to about 11 g/l histidine, and about 0 toabout 11 g/l ornithine. Although wider ranges are also within the scopeof the instant invention, including, but not limited to: about 0 toabout 30 g/l for arginine, about 0 to about 30 g/l for lysine, about 0to about 30 g/l histidine, and about 0 to about 30 g/l ornithine.

In certain embodiments, the cell culture media is supplemented withniacinamide, wherein the niacinamide is supplemented to achieve aniacinamide concentration of between about 0.2 and 3.0 mM, or betweenabout 0.4 and 3.0 mM, or between about 0.8 and 3.0 mM.

In certain embodiments, the cell culture media is supplemented withniacinamide wherein the niacinamide is supplemented in an amounteffective to reduce the amount of acidic species heterogeneity in aprotein or antibody sample by about 1%, 1.2%, 1.5%, 2%, 2.2%, 2.5%, 3%,3.2%, 3.5%, 4%, 4.2%, 4.5%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, and rangeswithin one or more of the preceding.

For example, and not by way of limitation, as detailed in Example 6.3,below, when the production medium employed in the example wassupplemented with niacinamide at a concentration of 1.6 mM, the totalamount of acidic species of adalimumab present in a cell culture sampleafter purification was reduced from 19.9% of a control sample to 15.9%of the sample purified from the cells cultured with the niacinamidesupplemented media. In a separate example, where the media wassupplemented with 3 mM niacinamide, the total amount of acidic speciesof adalimumab present in a cell culture sample after purification wasreduced from 27.0% of a control sample to 19.8% of the sample purifiedfrom the cells cultured with the niacinamide supplemented media.

In certain embodiments, the cell culture can be supplemented with acombination of niacinamide, calcium, e.g., CaCl₂, and/or one or more abasic amino acids. In certain embodiments the one or more basic aminoacids is arginine, lysine, histidine, ornithine, or combinations ofarginine or lysine with ornithine or of all four amino acids. In certainembodiments, the amino acids are provided as single peptides, asdipeptides, as tripeptides or as longer oligopeptides. In certainembodiments, the di-, tri-, and/or oligopeptides are individuallycomposed of a single amino acid, while in alternative embodiments, thedi-, tri-, and/or oligopeptides are individually composed of two or moreparticular amino acids. In certain embodiments, the amount of basicamino acid concentrations (after supplementation) in combination withcalcium in the cell culture is between about 0 to about 9 g/l forarginine, about 0 to about 11 g/l for lysine, about 0 to about 11 g/lhistidine, and about 0 to about 11 g/l ornithine. Although wider rangesare also within the scope of the instant invention, including, but notlimited to: about 0 to about 30 g/l for arginine, about 0 to about 30g/l for lysine, about 0 to about 30 g/l histidine, and about 0 to about30 g/l ornithine.

In certain embodiments, control over the amount of acidic species ofprotein produced by cell culture is exerted by supplementing the mediaof cells expressing the protein of interest medium supplements describedherein such that they can be included in the medium at the start ofculture, or can be added in a fed-batch or in a continuous manner. Thefeed amounts may be calculated to achieve a certain concentration basedon offline or online measurements. The addition of the supplement may bebased on measured amount of acidic species. Other salts of particularsupplements, e.g., calcium, may also be used, for example CalciumNitrate. The resulting media can be used in various cultivation methodsincluding, but not limited to, batch, fed-batch, chemostat andperfusion, and with various cell culture equipment including, but notlimited to, shake flasks with or without suitable agitation, spinnerflasks, stirred bioreactors, airlift bioreactors, membrane bioreactors,reactors with cells retained on a solid support or immobilized/entrappedas in microporous beads, and any other configuration appropriate foroptimal growth and productivity of the desired cell line.

In certain embodiments, control over amount and/or rate of formation ofacidic species is achieved by supplementing a clarified harvest. Forexample, but not by way of limitation, such clarified harvests can besupplemented as described above (e.g., with calcium, niacinamide, and/orbasic amino acids) to achieve a reduction the amount of acidic speciesand/or a reduction in the rate such acidic species form.

5.3.3 Adjusting Process Parameters to Control Acidic Species

In certain embodiments of the instant invention, control of acidicspecies heterogeneity can be attained by adjustment of pH of the cellculture run. In certain embodiments, such adjustment will be to decreasein the pH of the cell culture. Such decreases in the pH, can be of amagnitude of 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, and ranges within one ormore of the preceding, of the original amount.

In certain embodiments, pH is either increased or decreased in order toincrease or decrease the amount of acidic species and/or the rate atwhich such acidic species form. For example, but not by way oflimitation, a reduction in pH to 6.7 from a control pH of 7.1 can beemployed to decrease the acidic species during cell culture and the rateof acidic species formation in the context of a clarified harvest.

In certain embodiments, the pH is maintained in such a manner as toreduce the amount of acidic species in a protein or antibody sample byabout 1%, 1.2%, 1.5%, 2%, 2.2%, 2.5%, 3%, 3.2%, 3.5%, 4%, 4.2%, 4.5%,5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 100%, and ranges within one or more of thepreceding.

In certain embodiments, control over the amount of acidic species ofprotein produced by cell culture can be exerted by maintaining the pH ofthe cell culture expressing the protein of interest as described hereinalong with choice of suitable temperature or temperature shiftstrategies, for example, but not limited to, lower process temperatureof operation, temperature shift to a lower temperature or a temperatureshift at an earlier culture time point. These culture conditions can beused in various cultivation methods including, but not limited to,batch, fed-batch, chemostat and perfusion, and with various cell cultureequipment including, but not limited to, shake flasks with or withoutsuitable agitation, spinner flasks, stirred bioreactors, airliftbioreactors, membrane bioreactors, reactors with cells retained on asolid support or immobilized/entrapped as in microporous beads, and anyother configuration appropriate for optimal growth and productivity ofthe desired cell line. These may also be used in combination withsupplementation of culture media with amino acids, niacinamide, and/orcalcium salt, as described above.

5.3.4 Continuous/Perfusion Cell Culture Technology to Control AcidicSpecies

In certain embodiments of the instant invention, control of acidicspecies heterogeneity can be attained by the choice of cell culturemethodology. In certain embodiments, use of a continuous or perfusiontechnology may be utilized to achieve the desired control over acidicspecies heterogeneity. In certain embodiments, this may be attainedthrough choice of medium exchange rate (where the exchange rate is therate of exchange of medium in/out of a reactor). Such increases ordecreases in medium exchange rates may be of magnitude of 1%, 5%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 100%, and ranges within one or more of the preceding, ofthe original amount.

In certain, non-limiting, embodiments, maintenance of the mediumexchange rates (working volumes/day) of a cell culture run between 0 and20, or between 0.5 and 12 or between 1 and 8 or between 1.5 and 6 can beused to achieve the desired reduction in acidic species.

For example, and not by way of limitation, as detailed in Example 6.4,below, when the medium exchange rate was chosen to be 1.5, the acidicspecies was 8.1%. With further increase in exchange rates to 6, afurther reduction in acidic species to 6% was obtained.

In certain embodiments, the choice of cell culture methodology thatallows for control of acidic species heterogeneity can also include, forexample, but not by way of limitation, employment of an intermittentharvest strategy or through use of cell retention device technology.

5.4 PROTEIN PURIFICATION

5.4.1 Protein Purification Generally

In certain embodiments, the methods of the present invention can be usedin combination with techniques for protein purification to provide forthe production of a purified protein preparation, for example, apreparation comprising an antibody or an antigen binding fragmentthereof, from a mixture comprising a protein and at least oneprocess-related impurity or product-related substance.

For example, but not by way of limitation, once a clarified solution ormixture comprising the protein of interest, for example, an antibody orantigen binding fragment thereof, has been obtained, separation of theprotein of interest from the process-related impurities and/orproduct-related substances can be performed using a combination ofdifferent purification techniques, including, but not limited to,affinity separation steps, ion exchange separation steps, mixed modeseparation steps, and hydrophobic interaction separation steps. Theseparation steps separate mixtures of proteins on the basis of theircharge, degree of hydrophobicity, or size. In one aspect of theinvention, separation is performed using chromatography, includingcationic, anionic, and hydrophobic interaction. Several differentchromatography resins are available for each of these techniques,allowing accurate tailoring of the purification scheme to the particularprotein involved. The essence of each of the separation methods is thatproteins can be caused either to traverse at different rates down acolumn, achieving a physical separation that increases as they passfurther down the column, or to adhere selectively to the separationmedium, being then differentially eluted by different solvents. In somecases, the antibody is separated from impurities when the impuritiesspecifically adhere to the column and the antibody does not, i.e., theantibody is present in the flow through.

As noted above, accurate tailoring of a purification scheme relies onconsideration of the protein to be purified. In certain embodiments, theseparation steps of employed in connection with the cell culture methodsof the instant invention facilitate the separation of an antibody fromone or more process-related impurity and/or product-related substance.Antibodies that can be successfully purified using the methods describedherein include, but are not limited to, human IgA1, IgA2, IgD, IgE,IgG1, IgG2, IgG3, IgG4, and IgM antibodies, In certain embodiments,Protein A affinity chromatography can be useful, however, in certainembodiments, the use of Protein A affinity chromatography would proveuseful, for example in the context of the purification of IgG3antibodies, as IgG3 antibodies bind to Protein A inefficiently. Otherfactors that allow for specific tailoring of a purification schemeinclude, but are not limited to: the presence or absence of an Fc region(e.g., in the context of full length antibody as compared to an Fabfragment thereof) because Protein A binds to the Fc region; theparticular germline sequences employed in generating to antibody ofinterest; and the amino acid composition of the antibody (e.g., theprimary sequence of the antibody as well as the overallcharge/hydrophobicity of the molecule). Antibodies sharing one or morecharacteristic can be purified using purification strategies tailored totake advantage of that characteristic.

5.4.2 Primary Recovery and Virus Inactivation

In certain embodiments, it will be advantageous to subject a sampleproduced by the techniques of the instant invention to at least a firstphase of clarification and primary recovery. In addition, the primaryrecovery process can also be a point at which to reduce or inactivateviruses that can be present in the sample mixture. For example, any oneor more of a variety of methods of viral reduction/inactivation can beused during the primary recovery phase of purification including heatinactivation (pasteurization), pH inactivation, solvent/detergenttreatment, UV and γ-ray irradiation and the addition of certain chemicalinactivating agents such as β-propiolactone or e.g., copperphenanthroline as in U.S. Pat. No. 4,534,972, the entire teaching ofwhich is incorporated herein by reference.

The primary recovery may also include one or more centrifugation stepsto further clarify the sample mixture and thereby aid in purifying theprotein of interest. Centrifugation of the sample can be run at, forexample, but not by way of limitation, 7,000×g to approximately12,750×g. In the context of large scale purification, suchcentrifugation can occur on-line with a flow rate set to achieve, forexample, but not by way of limitation, a turbidity level of 150 NTU inthe resulting supernatant. Such supernatant can then be collected forfurther purification.

In certain embodiments, the primary recovery may also include the use ofone or more depth filtration steps to further clarify the sample matrixand thereby aid in purifying the antibodies produced using the cellculture techniques of the present invention. Depth filters containfiltration media having a graded density. Such graded density allowslarger particles to be trapped near the surface of the filter whilesmaller particles penetrate the larger open areas at the surface of thefilter, only to be trapped in the smaller openings nearer to the centerof the filter. In certain embodiments, the depth filtration step can bea delipid depth filtration step. Although certain embodiments employdepth filtration steps only during the primary recovery phase, otherembodiments employ depth filters, including delipid depth filters,during one or more additional phases of purification. Non-limitingexamples of depth filters that can be used in the context of the instantinvention include the Cuno™ model 30/60ZA depth filters (3M Corp.), and0.45/0.2 μm Sartopore™ bi-layer filter cartridges.

5.4.3 Affinity Chromatography

In certain embodiments, it will be advantageous to subject a sampleproduced by the techniques of the instant invention to affinitychromatography to further purify the protein of interest away fromprocess-related impurities and/or product-related substances. In certainembodiments the chromatographic material is capable of selectively orspecifically binding to the protein of interest. Non-limiting examplesof such chromatographic material include: Protein A, Protein G,chromatographic material comprising, for example, an antigen bound by anantibody of interest, and chromatographic material comprising an Fcbinding protein. In specific embodiments, the affinity chromatographystep involves subjecting the primary recovery sample to a columncomprising a suitable Protein A resin. In certain embodiments, Protein Aresin is useful for affinity purification and isolation of a variety ofantibody isotypes, particularly IgG1, IgG2, and IgG4. Protein A is abacterial cell wall protein that binds to mammalian IgGs primarilythrough their Fc regions. In its native state, Protein A has five IgGbinding domains as well as other domains of unknown function.

There are several commercial sources for Protein A resin. One suitableresin is MabSelect™ from GE Healthcare. A non-limiting example of asuitable column packed with MabSelect™ is an about 1.0 cm diameter×about21.6 cm long column (˜17 mL bed volume). This size column can be usedfor small scale purifications and can be compared with other columnsused for scale ups. For example, a 20 cm×21 cm column whose bed volumeis about 6.6 L can be used for larger purifications. Regardless of thecolumn, the column can be packed using a suitable resin such asMabSelect™.

5.4.4 Ion Exchange Chromatography

In certain embodiments, it will be advantageous to subject a sampleproduced by the techniques of the instant invention to ion exchangechromatography in order to purify the protein of interest away fromprocess-related impurities and/or product-related substances. Ionexchange separation includes any method by which two substances areseparated based on the difference in their respective ionic charges, andcan employ either cationic exchange material or anionic exchangematerial. For example, the use of a cationic exchange material versus ananionic exchange material is based on the localized charges of theprotein. Therefore, it is within the scope of this invention to employan anionic exchange step prior to the use of a cationic exchange step,or a cationic exchange step prior to the use of an anionic exchangestep. Furthermore, it is within the scope of this invention to employonly a cationic exchange step, only an anionic exchange step, or anyserial combination of the two.

In performing the separation, the initial protein mixture can becontacted with the ion exchange material by using any of a variety oftechniques, e.g., using a batch purification technique or achromatographic technique.

Anionic or cationic substituents may be attached to matrices in order toform anionic or cationic supports for chromatography. Non-limitingexamples of anionic exchange substituents include diethylaminoethyl(DEAE), quaternary aminoethyl (QAE) and quaternary amine (Q) groups.Cationic substituents include carboxymethyl (CM), sulfoethyl (SE),sulfopropyl (SP), phosphate (P) and sulfonate (5). Cellulose ionexchange resins such as DE23™, DE32™, DE52™, CM-23™, CM-32™, and CM-52™are available from Whatman Ltd. Maidstone, Kent, U.K. SEPHADEX®-basedand -locross-linked ion exchangers are also known. For example, DEAE-,QAE-, CM-, and SP-SEPHADEX® and DEAE-, CM- and S-SEPHAROSE® andSEPHAROSE® Fast Flow are all available from Pharmacia AB. Further, bothDEAE and CM derivitized ethylene glycol-methacrylate copolymer such asTOYOPEARL™ DEAE-650S or M and TOYOPEARL™ CM-650S or M are available fromToso Haas Co., Philadelphia, Pa.

5.4.5 Ultrafiltration/Diafiltration

In certain embodiments, it will be advantageous to subject a sampleproduced by the techniques of the instant invention to ultrafiltrationand/or diafiltration in order to purify the protein of interest awayfrom process-related impurities and/or product-related substances.Ultrafiltration is described in detail in: Microfiltration andUltrafiltration: Principles and Applications, L. Zeman and A. Zydney(Marcel Dekker, Inc., New York, N.Y., 1996); and in: UltrafiltrationHandbook, Munir Cheryan (Technomic Publishing, 1986; ISBN No.87762-456-9). A preferred filtration process is Tangential FlowFiltration as described in the Millipore catalogue entitled“Pharmaceutical Process Filtration Catalogue” pp. 177-202 (Bedford,Mass., 1995/96). Ultrafiltration is generally considered to meanfiltration using filters with a pore size of smaller than 0.1 μm. Byemploying filters having such small pore size, the volume of the samplecan be reduced through permeation of the sample buffer through thefilter while antibodies are retained behind the filter.

Diafiltration is a method of using ultrafilters to remove and exchangesalts, sugars, and non-aqueous solvents, to separate free from boundspecies, to remove low molecular-weight material, and/or to cause therapid change of ionic and/or pH environments. Microsolutes are removedmost efficiently by adding solvent to the solution being ultrafilteredat a rate approximately equal to the ultratfiltration rate. This washesmicrospecies from the solution at a constant volume, effectivelypurifying the retained protein. In certain embodiments of the presentinvention, a diafiltration step is employed to exchange the variousbuffers used in connection with the instant invention, optionally priorto further chromatography or other purification steps, as well as toremove impurities from the protein preparations.

5.4.6 Hydrophobic Interaction Chromatography

In certain embodiments, it will be advantageous to subject a sampleproduced by the techniques of the instant invention to hydrophobicinteraction chromatography in order to purify the protein of interestaway from process-related impurities and/or product-related substances.For example, a first eluate obtained from an ion exchange column can besubjected to a hydrophobic interaction material such that a secondeluate having a reduced level of impurity is obtained. Hydrophobicinteraction chromatography (HIC) steps, such as those disclosed herein,are generally performed to remove protein aggregates, such as antibodyaggregates, and process-related impurities.

In performing an HIC-based separation, the sample mixture is contactedwith the HIC material, e.g., using a batch purification technique orusing a column. Prior to HIC purification it may be desirable to removeany chaotropic agents or very hydrophobic substances, e.g., by passingthe mixture through a pre-column.

Whereas ion exchange chromatography relies on the charges of the proteinto isolate them, hydrophobic interaction chromatography uses thehydrophobic properties of the protein. Hydrophobic groups on the proteininteract with hydrophobic groups on the column. The more hydrophobic aprotein is the stronger it will interact with the column. Thus the HICstep removes host cell derived impurities (e.g., DNA and other high andlow molecular weight product-related species).

Hydrophobic interactions are strongest at high ionic strength,therefore, this form of separation is conveniently performed followingsalt precipitations or ion exchange procedures. Adsorption of theprotein of interest to a HIC column is favored by high saltconcentrations, but the actual concentrations can vary over a wide rangedepending on the nature of the protein and the particular HIC ligandchosen. Various ions can be arranged in a so-called soluphobic seriesdepending on whether they promote hydrophobic interactions (salting-outeffects) or disrupt the structure of water (chaotropic effect) and leadto the weakening of the hydrophobic interaction. Cations are ranked interms of increasing salting out effect as Ba⁺⁺; Ca⁺⁺; Mg⁺⁺; Li⁺; Cs⁺;Na⁺; K⁺; Rb⁺; NH4⁺, while anions may be ranked in terms of increasingchaotropic effect as P0⁻⁻⁻; S0₄ ⁻⁻; CH₃CO₃ ⁻; Cl⁻; Br⁻; NO₃ ⁻; ClO₄ ⁻;I⁻; SCN⁻.

In general, Na, K or NH₄ sulfates effectively promote ligand-proteininteraction in HIC. Salts may be formulated that influence the strengthof the interaction as given by the following relationship:(NH₄)₂SO₄>Na₂SO₄>NaCl>NH₄Cl>NaBr>NaSCN. In general, salt concentrationsof between about 0.75 and about 2 M ammonium sulfate or between about 1and 4 M NaCl are useful.

HIC columns normally comprise a base matrix (e.g., cross-linked agaroseor synthetic copolymer material) to which hydrophobic ligands (e.g.,alkyl or aryl groups) are coupled. A suitable HIC column comprises anagarose resin substituted with phenyl groups (e.g., a Phenyl Sepharose™column). Many HIC columns are available commercially. Examples include,but are not limited to, Phenyl Sepharose™ 6 Fast Flow column with low orhigh substitution (Pharmacia LKB Biotechnology, AB, Sweden); PhenylSepharose™ High Performance column (Pharmacia LKB Biotechnology, AB,Sweden); Octyl Sepharose™ High Performance column (Pharmacia LKBBiotechnology, AB, Sweden); Fractogel™ EMD Propyl or Fractogel™ EMDPhenyl columns (E. Merck, Germany); Macro-Prep™ Methyl or Macro-Prep™t-Butyl Supports (Bio-Rad, California); WP HI-Propyl (C3)™ column (J. T.Baker, New Jersey); and Toyopearl™ ether, phenyl or butyl columns(TosoHaas, PA).

5.4.7 Multimodal Chromatography

In certain embodiments, it will be advantageous to subject a sampleproduced by the techniques of the instant invention to multimodalchromatography in order to purify the protein of interest away fromprocess-related impurities and/or product-related substances. Multimodalchromatography is chromatography that utilizes a multimodal media resin.Such a resin comprises a multimodal chromatography ligand. In certainembodiments, such a ligand refers to a ligand that is capable ofproviding at least two different, but co-operative, sites which interactwith the substance to be bound. One of these sites gives an attractivetype of charge-charge interaction between the ligand and the substanceof interest. The other site typically gives electron acceptor-donorinteraction to and/or hydrophobic and/or hydrophilic interactions.Electron donor-acceptor interactions include interactions such ashydrogen-bonding, π-π, cation-π, charge transfer, dipole-dipole, induceddipole etc. Multimodal chromatography ligands are also known as “mixedmode” chromatography ligands.

In certain embodiments, the multimodal chromatography resin is comprisedof multimodal ligands coupled to an organic or inorganic support,sometimes denoted a base matrix, directly or via a spacer. The supportmay be in the form of particles, such as essentially sphericalparticles, a monolith, filter, membrane, surface, capillaries, etc. Incertain embodiments, the support is prepared from a native polymer, suchas cross-linked carbohydrate material, such as agarose, agar, cellulose,dextran, chitosan, konjac, carrageenan, gellan, alginate etc. To obtainhigh adsorption capacities, the support can be porous, and ligands arethen coupled to the external surfaces as well as to the pore surfaces.Such native polymer supports can be prepared according to standardmethods, such as inverse suspension gelation (S Hjerten: Biochim BiophysActa 79(2), 393-398 (1964). Alternatively, the support can be preparedfrom a synthetic polymer, such as cross-linked synthetic polymers, e.g.styrene or styrene derivatives, divinylbenzene, acrylamides, acrylateesters, methacrylate esters, vinyl esters, vinyl amides etc. Suchsynthetic polymers can be produced according to standard methods, seee.g. “Styrene based polymer supports developed by suspensionpolymerization” (R Arshady: Chimica e L′Industria 70(9), 70-75 (1988)).Porous native or synthetic polymer supports are also available fromcommercial sources, such as Amersham Biosciences, Uppsala, Sweden.

5.5 PHARMACEUTICAL COMPOSITIONS

The proteins, for example, antibodies and antibody-portions, producedusing the cell culture techniques of the instant invention can beincorporated into pharmaceutical compositions suitable foradministration to a subject. Typically, the pharmaceutical compositioncomprises a protein of the invention and a pharmaceutically acceptablecarrier. As used herein, “pharmaceutically acceptable carrier” includesany and all solvents, dispersion media, coatings, antibacterial andantifungal agents, isotonic and absorption delaying agents, and the likethat are physiologically compatible. Examples of pharmaceuticallyacceptable carriers include one or more of water, saline, phosphatebuffered saline, dextrose, glycerol, ethanol and the like, as well ascombinations thereof. In many cases, it is desirable to include isotonicagents, e.g., sugars, polyalcohols such as mannitol, sorbitol, or sodiumchloride in the composition. Pharmaceutically acceptable carriers mayfurther comprise minor amounts of auxiliary substances such as wettingor emulsifying agents, preservatives or buffers, which enhance the shelflife or effectiveness of the antibody or antibody portion.

The protein compositions of the invention can be incorporated into apharmaceutical composition suitable for parenteral administration. Theprotein can be prepared as an injectable solution containing, e.g.,0.1-250 mg/mL antibody. The injectable solution can be composed ofeither a liquid or lyophilized dosage form in a flint or amber vial,ampule or pre-filled syringe. The buffer can be L-histidineapproximately 1-50 mM, (optimally 5-10 mM), at pH 5.0 to 7.0 (optimallypH 6.0). Other suitable buffers include but are not limited to sodiumsuccinate, sodium citrate, sodium phosphate or potassium phosphate.Sodium chloride can be used to modify the toxicity of the solution at aconcentration of 0-300 mM (optimally 150 mM for a liquid dosage form).Cryoprotectants can be included for a lyophilized dosage form,principally 0-10% sucrose (optimally 0.5-1.0%). Other suitablecryoprotectants include trehalose and lactose. Bulking agents can beincluded for a lyophilized dosage form, principally 1-10% mannitol(optimally 24%). Stabilizers can be used in both liquid and lyophilizeddosage forms, principally 1-50 mM L-methionine (optimally 5-10 mM).Other suitable bulking agents include glycine, arginine, can be includedas 0-0.05% polysorbate-80 (optimally 0.005-0.01%). Additionalsurfactants include but are not limited to polysorbate 20 and BRIJsurfactants.

In one aspect, the pharmaceutical composition includes the protein at adosage of about 0.01 mg/kg-10 mg/kg. In another aspect, the dosages ofthe protein include approximately 1 mg/kg administered every other week,or approximately 0.3 mg/kg administered weekly. A skilled practitionercan ascertain the proper dosage and regime for administering to asubject.

The compositions of this invention may be in a variety of forms. Theseinclude, e.g., liquid, semi-solid and solid dosage forms, such as liquidsolutions (e.g., injectable and infusible solutions), dispersions orsuspensions, tablets, pills, powders, liposomes and suppositories. Theform depends on, e.g., the intended mode of administration andtherapeutic application. Typical compositions are in the form ofinjectable or infusible solutions, such as compositions similar to thoseused for passive immunization of humans with other antibodies. One modeof administration is parenteral (e.g., intravenous, subcutaneous,intraperitoneal, intramuscular). In one aspect, the protein isadministered by intravenous infusion or injection. In another aspect,the protein is administered by intramuscular or subcutaneous injection.

Therapeutic compositions typically must be sterile and stable under theconditions of manufacture and storage. The composition can be formulatedas a solution, microemulsion, dispersion, liposome, or other orderedstructure suitable to high drug concentration. Sterile injectablesolutions can be prepared by incorporating the active compound (i.e.,protein, antibody or antibody portion) in the required amount in anappropriate solvent with one or a combination of ingredients enumeratedabove, as required, followed by filtered sterilization. Generally,dispersions are prepared by incorporating the active compound into asterile vehicle that contains a basic dispersion medium and the requiredother ingredients from those enumerated above. In the case of sterile,lyophilized powders for the preparation of sterile injectable solutions,the methods of preparation are vacuum drying and spray-drying thatyields a powder of the active ingredient plus any additional desiredingredient from a previously sterile-filtered solution thereof. Theproper fluidity of a solution can be maintained, e.g., by the use of acoating such as lecithin, by the maintenance of the required particlesize in the case of dispersion and by the use of surfactants. Prolongedabsorption of injectable compositions can be brought about by includingin the composition an agent that delays absorption, e.g., monostearatesalts and gelatin.

The protein of the present invention can be administered by a variety ofmethods known in the art, one route/mode of administration issubcutaneous injection, intravenous injection or infusion. As will beappreciated by the skilled artisan, the route and/or mode ofadministration will vary depending upon the desired results. In certainembodiments, the active compound may be prepared with a carrier thatwill protect the compound against rapid release, such as a controlledrelease formulation, including implants, transdermal patches, andmicroencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Manymethods for the preparation of such formulations are patented orgenerally known to those skilled in the art. See, e.g., Sustained andControlled Release Drug Delivery Systems, J. R. Robinson, ed., MarcelDekker, Inc., New York, 1978, the entire teaching of which isincorporated herein by reference.

In certain aspects, a protein of the invention may be orallyadministered, e.g., with an inert diluent or an assailable ediblecarrier. The compound (and other ingredients, if desired) may also beenclosed in a hard or soft shell gelatin capsule, compressed intotablets, or incorporated directly into the subject's diet. For oraltherapeutic administration, the compounds may be incorporated withexcipients and used in the form of ingestible tablets, buccal tablets,troches, capsules, elixirs, suspensions, syrups, wafers, and the like.To administer a compound of the invention by other than parenteraladministration, it may be necessary to coat the compound with, orco-administer the compound with, a material to prevent its inactivation.

Supplementary active compounds can also be incorporated into thecompositions. In certain aspects, a protein of the invention isco-formulated with and/or co-administered with one or more additionaltherapeutic agents that are useful for treating disorders. For example,an antibody or antibody portion of the invention may be co-formulatedand/or co-administered with one or more additional antibodies that bindother targets (e.g., antibodies that bind other cytokines or that bindcell surface molecules). Furthermore, one or more antibodies of theinvention may be used in combination with two or more of the foregoingtherapeutic agents. Such combination therapies may advantageouslyutilize lower dosages of the administered therapeutic agents, thusavoiding possible toxicities or complications associated with thevarious monotherapies. It will be appreciated by the skilledpractitioner that when the protein of the invention are used as part ofa combination therapy, a lower dosage of protein may be desirable thanwhen the protein alone is administered to a subject (e.g., a synergistictherapeutic effect may be achieved through the use of combinationtherapy which, in turn, permits use of a lower dose of the protein toachieve the desired therapeutic effect).

It should be understood that the protein of the invention can be usedalone or in combination with an additional agent, e.g., a therapeuticagent, said additional agent being selected by the skilled artisan forits intended purpose. For example, the additional agent can be atherapeutic agent art-recognized as being useful to treat the disease orcondition being treated by the protein of the present invention. Theadditional agent also can be an agent which imparts a beneficialattribute to the therapeutic composition, e.g., an agent which effectsthe viscosity of the composition.

Dosage regimens may be adjusted to provide the optimum desired response(e.g., a therapeutic or prophylactic response). For example, a singlebolus may be administered, several divided doses may be administeredover time or the dose may be proportionally reduced or increased asindicated by the exigencies of the therapeutic situation. In certainembodiments it is especially advantageous to formulate parenteralcompositions in dosage unit form for ease of administration anduniformity of dosage. Dosage unit form as used herein refers tophysically discrete units suited as unitary dosages for the mammaliansubjects to be treated; each unit comprising a predetermined quantity ofactive compound calculated to produce the desired therapeutic effect inassociation with the required pharmaceutical carrier. The specificationfor the dosage unit forms of the invention are dictated by and directlydependent on (a) the unique characteristics of the active compound andthe particular therapeutic or prophylactic effect to be achieved, and(b) the limitations inherent in the art of compounding such an activecompound for the treatment of sensitivity in individuals.

An exemplary, non-limiting range for a therapeutically orprophylactically effective amount of a protein of the invention is0.01-20 mg/kg, or 1-10 mg/kg, or 0.3-1 mg/kg. It is to be noted thatdosage values may vary with the type and severity of the condition to bealleviated. It is to be further understood that for any particularsubject, specific dosage regimens should be adjusted over time accordingto the individual need and the professional judgment of the personadministering or supervising the administration of the compositions, andthat dosage ranges set forth herein are exemplary only and are notintended to limit the scope or practice of the claimed composition.

6. EXAMPLES 6.1 Method for Reducing the Extent of Acidic Species in CellCulture by the Addition of Medium Components

Production of recombinant proteins by host cells can result inproduct-related charge heterogeneities present in the population ofproteins produced by the cells. The presence of acidic species in thepopulation of proteins is an example of a product-related chargeheterogeneity. Control of the amount of acidic species present in thepopulation of proteins produced by the host cells can be accomplished bymodifying the culture conditions of the host cells.

6.1.1 Materials and Methods

Cell Source and Adaptation Cultures

Three adalimumab producing cell lines, one mAb1 producing cell line andone mAb2 producing were employed in the studies covered here. Foradalimumab producing cell lines, cells were cultured in their respectivegrowth media (chemically defined media (media 1) or a hydrolysate basedmedia (media 2 or media 3)) in a combination of vented non-baffled shakeflasks (Corning) on a shaker platform at 110 RPM (cell line 1), 180 RPM(cell line 2), 140 RPM (cell line 3) and 10 L or 20 L wave bags (GE).For experiments with cells in the hydrolysate based media (media 3),cells were thawed in media 1 and then adapted to media 3 over a fewpassages. Cultures were propagated in a 35° C., 5% CO₂ incubator forcell line 1 and 2 and in a 36° C., 5% CO₂ incubator for cell line 3 inorder to obtain the required number of cells to be able to initiateproduction stage cultures.

For the mAb1 producing cell line, cells were cultured in chemicallydefined growth media (media 1) in a combination of vented non-baffledshake flasks (Corning) on a shaker platform at 130 RPM and 20 L wavebags (GE). Cultures were propagated in a 36° C., 5% CO₂ incubator toobtain the required number of cells to be able to initiate productionstage cultures.

For the mAb2 producing cell line, cells were cultured in chemicallydefined growth media (media 1) in a combination of vented non-baffledshake flasks (Corning) on a shaker platform at 140 RPM and 20 L wavebags (GE). Cultures were propagated in a 35° C., 5% CO₂ incubator toobtain the required number of cells to be able to initiate productionstage cultures.

Cell Culture Media

Growth and production media were prepared from either a chemicallydefined media formulation (media 1) or hydrolysate-based mediumformulations (media 2 and media 3). For preparation of the media 1, themedia (IVGN GIA-1, a proprietary basal media formulation fromInvitrogen) was supplemented with L-glutamine, sodium bicarbonate,sodium chloride, and methotrexate solution. Production media consistedof all the components in the growth medium, excluding methotrexate. Forcell line 1, both growth and production medium were also supplementedwith insulin. For mAB1 and mAB2 producing cell lines, the growth mediumwere also supplemented with insulin.

For the hydrolysate-based formulation (media 2), the growth media wascomposed of PFCHO (proprietary chemically defined formulation fromSAFC), Dextrose, L-Glutamine, L-Asparagine, HEPES, Poloxamer 188, FerricCitrate, Recombinant Human Insulin, Yeast® late (BD), Phytone Peptone(BD), Mono- and Di-basic Sodium Phosphate, Sodium Bicarbonate, SodiumChloride and methotrexate. Production media consisted of all thecomponents listed in the growth medium, excluding methotrexate.

For the hydrolysate-based formulation (media 3), the growth media wascomposed of OptiCHO (Invitrogen), L-Glutamine, Yeast® late (BD), PhytonePeptone (BD) and methotrexate. Production media consisted of all thecomponents listed in the growth medium, excluding methotrexate.

Amino acids used for the experiments were reconstituted in Milli-Q waterto make a 100 g/L stock solution, which was subsequently supplemented toboth growth and production basal media. After addition of amino acids,media was brought to a pH similar to unsupplemented (control) mediausing 5N hydrochloric acid/5N NaOH, and it was brought to an osmolalitysimilar to unsupplemented (control) media by adjusting the concentrationof sodium chloride.

Calcium Chloride Dihydrate (Sigma or Fluka) used for the experimentswere reconstituted in Milli-Q water to make a stock solution, which wassubsequently supplemented to the production basal media. After additionof calcium chloride, media was brought to a pH similar tonon-supplemented (control) media using 6N hydrochloric acid/5N NaOH, andit was brought to an osmolality similar to non-supplemented (control)media by adjusting the concentration of sodium chloride.

Niacinamide (Sigma or Calbiochem) used for the experiments werereconstituted in Milli-Q water to make a stock solution, which wassubsequently supplemented to the production basal media. After additionof niacinamide, media was brought to a pH similar to non-supplemented(control) media using 6N hydrochloric acid/6N NaOH, and it was broughtto an osmolality similar to non-supplemented (control) media byadjusting the concentration of sodium chloride.

All media was filtered through Corning 1 L filter systems (0.22 μm PES)and stored at 4° C. until usage.

TABLE 2 List of medium additives supplemented to culture media CatalogNo./Source Medium of medium additive supplements Arginine Sigma, A8094Lysine Calbiochem, 4400 Histidine Sigma, H5659 Ornithine Sigma, 06503Calcium Fulka, 21097 Chloride Sigma, C8106 Niacinamide Calbiochem,481907 Sigma, N0636 Production cultures

Production cultures were initiated either in 500 ml shake flasks(Corning) or in 3 L Bioreactors (Applikon). For shake flask experiments,duplicate 500 mL Corning vented non-baffled shake flasks (200 mL workingvolume) were used for each condition. The shake flasks were kept inincubators either maintained at 35° C. or 36° C. and 5% CO₂ on shakerplatforms that were either set at 110 rpm for adalimumab producing cellline 1, 180 rpm for adalimumab producing cell line 2, 140 rpm foradalimumab producing cell line 3, for 130 rpm for mAB1 producing cellline, or 140 rpm for mAB2 producing cell line. For the bioreactorexperiments, 3 L bioreactors (1.5 L working volume) were run at 35° C.,30% DO, 200 rpm, pH profile from 7.1 to 6.9 in three days and pH 6.9thereafter. In all experiments, the cells were transferred from the seedtrain to the production stage at a split ratio of 1:5.

Cultures were run in either batch or fed-batch mode. In the batch mode,cells were cultured in the respective production medium. 1.25% (v/v) of40% glucose stock solution was fed when the media glucose concentrationreduced to less than 3 g/L. In the fed-batch mode, cultures were runwith either the IVGN feed (proprietary chemically defined feedformulation from Invitrogen) as per the following feed schedule −(4%(v/v)−day 6, day 7, and day 8, respectively) along with 10×Ex-Cell PFCHOfeed (proprietary chemically defined formulation)−3% (v/v) on day 3. Thecultures were also fed with 1.25% (v/v) of 40% glucose stock solutionwhen the glucose concentration was below 3.0 g/l.

Retention samples for titer analysis, of 2×1.5 mL, were collected dailyfor the bioreactor experiments (section 2.2.4) beginning on Day 8, andfrozen at −80° C. The samples taken from each were later submitted fortiter analysis.

The harvest procedure of the shake flasks and reactors involvedcentrifugation of the culture sample at 3,000 RPM for 30 min and storageof supernatant in PETG bottles at −80° C. before submission for proteinA purification and WCX-10 analysis.

WCX-10 Assay

This method is employed towards the quantification of the acidic speciesand other charge variants present in cell culture harvest samples.Cation exchange chromatography was performed on a Dionex ProPac WCX-10,Analytical column (Dionex, CA).

For adalimumab and mAB1 samples, the mobile phases used were 10 mMSodium Phosphate dibasic pH 7.5 (Mobile phase A) and 10 mM SodiumPhosphate dibasic, 500 mM Sodium Chloride pH 5.5 (Mobile phase B). Abinary gradient (94% A, 6% B: 0-20 min; 84% A, 16% B: 20-22 min; 0% A,100% B: 22-28 min; 94% A, 6% B: 28-34 min) was used with detection at280 nm.

For mAb2 samples, the mobile phases used were 20 mM(4-Morpholino)ethanesulfonic Acid Monohydrate (MES) pH 6.5 (Mobile phaseA) and 20 mM MES, 500 mM Sodium Chloride pH 6.5 (Mobile phase B). Anoptimized gradient (minute/% B): 0/3, 1/3, 46/21, 47/100, 52/100, 53/3,58/3 was used with detection at 280 nm.

Quantitation is based on the relative area percent of detected peaks.The peaks that elute at relative residence time earlier than the mainpeak corresponding to the drug product are together represented as theacidic peaks (FIG. 1).

Lysine-C Peptide Mapping for MGO Quantification

Typical trypsin digestion employed almost universally for peptidemapping cuts a denatured, reduced and alkylated protein at the carboxylside of the two basic amino acids, lysine and arginine. Methylglyoxal isa small molecule metabolite derived as a glycolysis byproduct which canmodify arginine residues. A modification of an arginine prevents trypsinfrom cutting this site and results in a mis-cleavage. The challenge ofquantifying the amount of MGO modified peptide is that it is notcompared to an equivalent non-modified peptide but rather two parentalcleaved peptides which will likely have different ionization potentialthan the modified peptide. In order to determine a truly accurate directmeasurement of an MGO-modified peptide, it must be compared to itsnon-modified counterpart and expressed as a percent. Usingendoproteinase Lysine-C as an alternative enzyme, cleavages only occurat lysine residues. The result is a direct comparison of the samepeptide with and without an MGO modification which provides a highdegree of accuracy in quantifying even trace levels of the modifiedspecies.

Procedure: Samples are diluted to a nominal concentration of 4 mg/mL. 8M guanidine-HCl is added to the sample in a 3:1 ratio resulting in a 1mg/mL concentration in 6M guanidine-HCl. The samples are reduced with 10mM final conc. DTT for 30 minutes at 37° C. followed by an alkylationwith 25 mM final cone. iodoacetic acid for 30 minutes at 37° C. in thedark. The samples are then buffer exchanged into 10 mM Tris pH 8.0 usingNAP-5 columns. The samples are then digested for 4 hours at 37° C. usingendoproteinase Lys-C at an enzyme to protein ratio of 1:20. The digestis quenched by adding 5 μL of formic acid to each sample. Samples areanalyzed by LC/MS peptide mapping. Briefly, 50 μl, of sample is loadedonto a Waters BEH C18 1.7μ 1.0×150 mm UPLC column with 98% 0.08% formicacid, 0.02% TFA in water and 2% 0.08% formic acid, 0.02% TFA inacetonitrile. The composition is changed to 65% 0.08% formic acid, 0.02%TFA in water and 35% 0.08% formic acid, 0.02% TFA in acetonitrile in 135minutes using a Waters Acquity UPLC system. Eluting peaks are monitoredusing a Thermo Scientific LTQ-Orbitrap Mass Spectrometer. Specific masstraces are extracted for both modified and non-modified peptides inorder to accurately quantify the total amount of MGO modification ateach site. Mass spectra are also analyzed for the specific region of thechromatogram to confirm the peptide identity. An example data set isshown in FIG. 140.

6.1.2 Results

Effect of Arginine Supplementation to Cell Culture Media

The addition of arginine was tested in several experimental systemscovering multiple cell lines, media and monoclonal antibodies. Followingis a detailed description of two representative experiments where twodifferent adalimumab producing cell lines were cultured in a chemicallydefined media (media 1).

Cell line 2 was cultured in media 1 with different total amounts ofarginine (1 (control), 1.25, 1.5, 2, 3, 5, 9 g/l). The cultures wereperformed in shake flasks in batch format with only glucose feed asdescribed in the materials and methods. The cells grew to maximum viablecell densities (VCD) in the range of 18-22×10⁶ cells/ml for thedifferent conditions tested. The growth and viability profiles werecomparable between the different test conditions, although a slightdecrease in viable cell density profile was observed in samples with the9 g/l arginine test condition (FIGS. 1, 2). The harvest titers werecomparable between the conditions (FIG. 3). On Day 10 and Day 12 ofculture, duplicate shake flasks for each of the conditions wereharvested and then subsequently analyzed using WCX-10 post protein Apurification and the percentages of total peaks) area corresponding tothe acidic species were quantified (FIG. 4, 5). The percentage of acidicspecies in the control sample was as high as 19.7% on day 10. In thesample with the highest total concentration of arginine in thisexperiment (9 g/l), the percentage of acidic species was reduced to12.2%. A dose dependent decrease in acidic species was observed in testconditions with arginine concentrations beyond 2 g/l (FIG. 4). A similartrend in reduction of acidic species with arginine increase was alsoobserved in the day 12 harvest samples (FIG. 5). Further, while theextent of acidic species in the 1 g/l arginine samples increased from19.7% (day 10 harvest) to 25.5% (day 12 harvest), this increase in the 9g/l arginine test condition was significantly smaller from 12.2% (day 10harvest) to 13.9% (day 12 harvest). Thus, the increase of total arginineled to a reduction in the extent of total acidic species at a particulartime point in culture as well the rate of increase of acidic specieswith time of culture.

Cell line 3 was cultured in media 1 with different total amounts ofarginine (1 (control), 3, 5, 7, 9 g/l). The cultures were performed inshake flasks in batch format with only glucose feed as described in thematerials and methods. The cells grew to maximum viable cell densities(VCD) in the range of 7-10×10⁶ cells/ml for the different conditionstested. The growth and viability profiles were comparable between thedifferent test conditions, although a slight decrease in viable celldensity and viability profiles was observed in samples with the 9 g/larginine condition (FIG. 6, 7). The product titer was also comparablebetween all conditions (FIG. 8). On Day 10 of culture, duplicate shakeflasks for each of the conditions were harvested and then subsequentlyanalyzed using WCX-10 post protein A purification and the percentages oftotal peak(s) area corresponding to the acidic species were quantified(FIG. 9). The percentage of acidic species in the control sample was ashigh as 23.3% on day 10. In the sample with the highest totalconcentration of arginine in this experiment (9 g/l), the percentage ofacidic species was reduced to 17.0%. A dose dependent decrease in acidicspecies was observed in conditions with higher concentrations ofarginine.

Additional experiments were performed with multiple cell lines inchemically defined or hydrolysate based media to demonstrate the widerange of applicability of this method. The experimental setup for eachof these experiments was similar to that described above. The summariesof results of the different experiments performed for adalimumab aresummarized in FIGS. 10, 11, 12. A reduction in acidic species withincreased arginine concentration was also observed in each case.

In addition to adalimumab, the utility of this method for acidic speciesreduction was also demonstrated for processes involving two other mABproducing cell lines. The experimental setup for each of theseexperiments was similar to that described in section above and in thematerials and methods. The reduction of acidic species with increasedarginine concentration for experiments corresponding to each mAB issummarized in FIG. 13, 14. For mAB2, a significant reduction in acidicspecies was only observed at arginine concentration of 9 g/l.

In the application assigned attorney docket no. 082254.0238, we describethe utility of arginine supplementation to culture media towardsmodulation of the lysine variant distribution. It is possible that afraction of acidic species also shifted along with shift in lysinevariants (from Lys 0 to Lys1 and Lys2), in addition to the fraction ofacidic species that is completely removed from the entire proteinpopulation. To estimate the acidic species reduction that is independentof this redistribution of lysine variants, protein A eluate samples froma representative set of arginine supplementation experiments werepre-treated with the enzyme carboxypeptidase before WCX-10. One set ofsamples from adalimumab experiment and another set of samples from amAB2 experiment were used for this analysis. The carboxypeptidasetreatment of the samples resulted in the cleavage of the C-terminallysine residues as demonstrated by the complete conversion of Lys1/Lys2to Lys 0 in each of these samples (data not shown here). As a result ofthis conversion, the acidic species quantified in these samplescorresponded to an aggregate sum of acidic species that would beexpected to also include those species that may have previously shiftedcorresponding to the lysine variant shift and perhaps gone unaccountedfor in the samples that were not treated with carboxypeptidase prior toWCX-10. A dose dependent reduction in acidic species was observed in thecarboxypeptidase treated samples with increasing concentration arginine(FIG. 15, 16). This suggests that the acidic species reduction describedhere is not completely attributed to a probable shift of the acidicspecies corresponding to the lysine variant redistribution.

Effect of Lysine Supplementation to Cell Culture Media

The addition of lysine was tested in several experimental systemscovering multiple cell lines, media and monoclonal antibodies. Followingis a detailed description of two representative experiments where twodifferent cell lines were cultured in a chemically defined media(media 1) for the production of adalimumab.

Cell line 2 was cultured in media 1 with different total concentrationsof lysine (1 (control), 5, 7, 9, 11 g/l). The cultures were performed inshake flasks in batch format with only glucose feed as described in thematerials and methods. The cells grew to maximum viable cell densities(VCD) in the range of 17-23×10⁶ cells/ml for the different conditionstested. A slight dose dependent decrease in viable cell density profilewas observed in all samples with respect to the control sample (FIG.17). The viability profiles were comparable between the conditions (FIG.18). On Days 10 and 11 of culture samples were collected for titeranalysis (FIG. 19). The titers for all conditions were comparable. OnDay 11 of culture, duplicate shake flasks for each of the conditionswere harvested and then subsequently analyzed using WCX-10 post proteinA purification and the percentages of total peak(s) area correspondingto the acidic species were quantified (FIG. 20). The percentage ofacidic species in the control was as high as 26.5%. In the sample withthe highest tested concentration of lysine in this experiment (11 g/l),the percentage of acidic species was reduced to 15.0%. A dose dependentdecrease in acidic species was observed in test conditions with highertotal concentrations of lysine.

Cell line 3 was cultured in media 1 with different total concentrationsof lysine (1 (control), 3, 5, 7, 9, 11 g/l). The cultures were performedin shake flasks in batch format with only glucose feed as described inthe materials and methods. The cells grew to maximum viable celldensities (VCD) in the range of 9.5-11.5×10⁶ cells/ml for the differentconditions tested. The growth and viability profiles were comparablebetween the different test conditions, although a slight decrease inviable cell density and viability profiles was observed in samples withhigher lysine concentrations than that in the control sample (FIG. 21,22). On Days 10, 11 and 12 of culture samples were collected for titeranalysis (FIG. 23). The titers for all conditions were comparable. OnDay 12 of culture, duplicate shake flasks for each of the conditionswere harvested and then subsequently analyzed using WCX-10 post proteinA purification and the percentages of total peak(s) area correspondingto the acidic species were quantified (FIG. 24). The percentage ofacidic species in the control sample was as high as 26.6%. In the samplewith the highest tested concentration of lysine in this experiment (11g/l) the percentage of acidic species was reduced to 18.1%. A dosedependent decrease in acidic species was observed in test conditionswith higher total concentrations of lysine.

Additional experiments were performed with multiple cell lines inchemically defined or hydrolysate based media to demonstrate the widerange of applicability of this method. The experimental setup for eachof these experiments was similar to that described above and inmaterials and methods section. The summaries of results of the differentexperiments performed for adalimumab are summarized in FIGS. 25, 26, 27.A reduction in acidic species with increased lysine concentration wasalso observed in each case.

In addition to adalimumab, the utility of this method for acidic speciesreduction was also demonstrated for processes involving two other mABs.The experimental setup for each of these experiments was similar to thatdescribed above and in the materials and methods section. The reductionof acidic species with lysine addition for experiments corresponding toeach mAB is summarized in FIGS. 28, 29. For mAB2, a significantreduction in acidic species was only observed at lysine concentration of11 g/l.

In the application assigned attorney docket no. 082254.0238, we describethe utility of lysine supplementation to culture media towardsmodulation of the lysine variant distribution. To estimate the acidicspecies reduction that is independent of this redistribution of lysinevariants, protein A eluate samples from a representative set of lysinesupplementation experiments were pre-treated with the enzymecarboxypeptidase before WCX-10. One set of samples from adalimumabexperiment and another set of samples from a mAB2 experiment were usedfor this analysis. The carboxypeptidase treatment of the samplesresulted in the cleavage of the C-terminal lysine residues asdemonstrated by the conversion of Lys1/Lys2 to Lys 0 in each of thesesamples (data not shown here). As a result of this conversion, theacidic species quantified in these samples corresponded to an aggregatesum of acidic species that would be expected to also include thosespecies that may have previously shifted corresponding to the lysinevariant shift and perhaps gone unaccounted for in the samples that werenot treated with carboxypeptidase prior to WCX-10. A dose dependentreduction in acidic species was observed in the carboxypeptidase treatedsamples with increasing concentration of lysine for the adalimumabsamples from 26.8% in the non-supplemented sample to 21.1% in the 10 g/lLysine supplemented sample, a reduction of 5.7% in total acidic species(FIG. 30). Similar results were also observed for the mA2 samples (FIG.31). This suggests that the acidic species reduction described here isnot completely attributed to a probable shift of the acidic speciescorresponding to the lysine redistribution.

Effect of Histidine Supplementation to Cell Culture Media

The addition of histidine was tested in several experimental systemscovering multiple cell lines, media and monoclonal antibodies. Followingis a detailed description of two representative experiments where twodifferent cell lines were cultured in a chemically defined media(media 1) for the production of adalimumab.

Cell line 2 was cultured in media 1 with different total concentrationsof histidine (0 (control), 4, 6, 8, 10 g/l). The cultures were performedin shake flasks in batch format with only glucose feed as described inthe materials and methods. The cells grew to maximum viable celldensities (VCD) in the range of 12-22×10⁶ cells/ml for the differentconditions tested. A dose dependent decrease in viable cell densityprofile was observed with the 10 g/l histidine condition havingsignificant reduction in growth (FIG. 32). A corresponding effect onviability was also observed (FIG. 33). On Days 10, 11 and 12 of culturesamples were collected for titer analysis and reported for the harvestday for each sample (FIG. 34). There was a small dose dependent decreasein titers for conditions with histidine supplementation. On Days 11-12,duplicate shake flasks were harvested and then subsequently analyzedusing WCX-10 post protein A purification and the percentages of totalpeak(s) area corresponding to the acidic species were quantified (FIG.35). The percentage of acidic species in the control sample was as highas 26.5%. In the sample with the highest tested concentration ofhistidine in this experiment (10 g/l), the percentage of acidic specieswas reduced to 15.6%. A dose dependent decrease in acidic species wasobserved in test conditions with increased histidine concentrations.

Cell line 3 was cultured in media 1 with different total concentrationsof histidine (0 (control), 2, 4, 6, 8 g/l). The cultures were performedin shake flasks in batch format with only glucose feed as described inthe materials and methods. The cells grew to maximum viable celldensities (VCD) in the range of 6-10×10⁶ cells/ml for the differentconditions tested. A dose dependent decrease in viable cell densityprofile was observed in all conditions with histidine concentrationshigher than that in the control (FIG. 36). The viability profiles weremore comparable between conditions with this cell line (FIG. 37). On Day12 of culture, samples were collected for titer analysis (FIG. 38). Thetiters for all conditions were comparable. On Day 12 of culture,duplicate shake flasks for each of the conditions were harvested andthen subsequently analyzed using WCX-10 post protein A purification andthe percentages of total peak(s) area corresponding to the acidicspecies were quantified (FIG. 39). The percentage of acidic species inthe control sample was 26.2%. In the sample with the highest testedconcentration of histidine in this experiment (8 g/l), the percentage ofacidic species was reduced to 20.0%. A dose dependent decrease in acidicspecies was observed in test conditions with increased histidineconcentration.

Additional experiments were performed with multiple cell lines inchemically defined or hydrolysate based media to evaluate the wide rangeof applicability of this method. The experimental setup for each ofthese experiments was similar to that described above and in thematerials and methods section. The summaries of results of the differentexperiments performed for adalimumab are summarized in FIGS. 40, 41, 42.A reduction in acidic species with increased histidine concentration wasobserved with cell line 1 in media 1 (FIG. 40) and with cell line 2 inmedia 3 (FIG. 42). For cell line 2 in media 3, a dose dependentreduction in acidic species was observed upto 4 g/l histidine, with nofurther significant reduction at higher concentrations of histidine(FIG. 42). For cell line 1, media 2, no significant reduction of acidicspecies was observed within the histidine concentration range (0-4 g/l)(FIG. 41). In addition to adalimumab, the utility of this method foracidic species reduction was also demonstrated for processes involvingtwo other mABs. The experimental setup for each of these experiments wassimilar to that described above and in the materials and methodssection. The reduction of acidic species with increased histidineconcentration for experiments corresponding to each mAB is summarized inFIGS. 43, 44. For mAB2, in contrast with the results reported witharginine and lysine supplementation shown previously, a clearsignificant dose dependent reduction in total acidic species from 28.1%in the control to 21.5% in 4 g/l histidine sample was observed.

In the application assigned attorney docket no. 082254.0238, we alsodescribe the utility of increased histidine to culture media towardsmodulation of the lysine variant distribution. To estimate the acidicspecies reduction that is independent of this redistribution of lysinevariants, protein A eluate samples from a representative set ofhistidine supplementation experiments were also pre-treated with theenzyme carboxypeptidase before WCX-10. One set of samples fromadalimumab experiment and another set of samples from a mAB2 experimentwere used for this analysis. The carboxypeptidase treatment of thesamples resulted in the cleavage of the C-terminal lysine residues asdemonstrated by the complete conversion of Lys1/Lys2 to Lys 0 in each ofthese samples (data not shown here). A dose dependent reduction inacidic species was observed in the carboxypeptidase treated samples withincreasing concentration of histidine (FIG. 45, 46). This suggests thatthe acidic species reduction described here is not completely attributedto a probable shift of the acidic species corresponding to the lysineredistribution.

Effect of Ornithine Supplementation to Cell Culture Media

The addition of ornithine was tested in several experimental systemscovering multiple cell lines, media and monoclonal antibodies. Followingis a detailed description of two representative experiments where twodifferent cell lines were employed in a chemically defined media(media 1) for the production of adalimumab.

Cell line 2 was cultured in media 1 with different total concentrationsof ornithine (0 (control), 4, 6, 8, 10 g/l). The cultures were performedin shake flasks in batch format with only glucose feed as described inthe materials and methods. The cells grew to maximum viable celldensities (VCD) in the range of 15-22×10⁶ cells/ml for the differentconditions tested, A slight decrease in viable cell density withornithine supplementation was observed (FIG. 47). Correspondingdifferences in the viability profiles were also observed (FIG. 48). OnDay 11 of culture, samples were collected for titer analysis (FIG. 49).The titers for all conditions were comparable. On Day 11, duplicateshake flasks were harvested for each condition and then subsequentlyanalyzed using WCX-10 post protein A purification and the percentages oftotal peak(s) area corresponding to the acidic species were quantified(FIG. 50). The percentage of acidic species in the control sample was26.5%. In the sample with the highest tested concentration of ornithinein this experiment (10 g/l), the percentage of acidic species wasreduced to 16.1%. A dose dependent decrease in acidic species wasobserved in test conditions with increased ornithine concentration.

Cell line 3 was cultured in media 1 supplemented with different totalconcentrations of ornithine (0 (control), 2, 4, 6, 8 g/l). The cultureswere performed in shake flasks in batch format with only glucose feed asdescribed in the materials and methods. The cells grew to maximum viablecell densities (VCD) in the range of 9.5-11.5×10⁶ cells/ml for thedifferent conditions tested. The viable cell density and viabilityprofiles were comparable (FIG. 51, 52). On Day 12 of culture, sampleswere collected for titer analysis (FIG. 53). The titers for allconditions were comparable. On Day 12 of culture, duplicate shake flasksfor each of the conditions were harvested and then subsequently analyzedusing WCX-10 post protein A purification and the percentages of totalpeak(s) area corresponding to the acidic species were quantified (FIG.54). The percentage of acidic species in the control sample was 24.8%.In the sample with the highest tested concentration of ornithine in thisexperiment (8 g/l), the percentage of acidic species was reduced to20.5%. A dose dependent decrease in acidic species was observed in testconditions with increased ornithine concentration.

Additional experiments were performed with multiple cell lines inchemically defined or hydrolysate based media to evaluate the wide rangeof applicability of this method. The experimental setup for each ofthese experiments was similar to that described above and in thematerials and methods section. The summaries of results of the differentexperiments performed for adalimumab are summarized in FIGS. 55, 56 and57. For cell line 1 in media 1, a dose dependent reduction was observed(FIG. 55). However, for cell line 1 in media 2, a hydrolysate media, nosignificant reduction in acidic species was observed across theconditions (FIG. 56). For cell line 2 in media 3, a reduction in acidicspecies from 22.1% in the control sample to 18.7% in the 2 g/l ornithinesample with no further reduction at higher ornithine concentrations wasobserved (FIG. 57).

In addition to adalimumab, the utility of this method for acidic speciesreduction was also demonstrated for processes involving two other mABs.The experimental setup for each of these experiments was similar to thatdescribed in section above and in the materials and method section. Thereduction of acidic species with ornithine addition for experimentscorresponding to each mAB is summarized in FIG. 58, 59. In the case ofmAB1, a 7.3% dose dependent reduction in total acidic species wasobserved within the concentration range tested. For mAB2, about 2%reduction was observed in the 1 g/l ornithine concentration sample withminimum further reduction at higher ornithine concentrations.

Similar to the analysis conducted with the other amino acids, protein Aeluate samples from a representative set of ornithine experiments werealso pre-treated with the enzyme carboxypeptidase before WCX-10. One setof samples from adalimumab experiment and another set of samples from amAB2 experiment were used for this analysis. A dose dependent reductionin acidic species was observed in the carboxypeptidase treated sampleswith increasing concentration of ornithine (FIG. 60, 61). The percentageof acidic species was also comparable between an untreated and acarboxypeptidase treated sample for a particular concentration ofornithine. This suggests that the acidic species reduction isindependent of any probable shift of the acidic species that may becorresponding to any lysine redistribution.

Effect of Increasing a Combination of Arginine, Lysine, Histidine,Ornithine to Cell Culture Media

In this experiment, the combined use of the four amino acids arginine,lysine, histidine and ornithine for acidic species reduction isdemonstrated. The experiment described here was performed usingadalimumab producing cell line 2 in chemically defined media (media 1).The concentration range for arginine and lysine in this experiment was1-3 g/l while the concentration range for histidine and ornithine inthis experiment was between 0-2 g/l. In comparison to the lowerconcentrations, or conditions where a single amino acid concentrationwas increased, a further reduction in total acidic species was observedin conditions where combinations of amino acids were increased in themedia (FIG. 62). A progressive decrease was observed in total acidicspecies when more amino acids were increased in combination. Thepercentage of acidic species was reduced from 21.9% in the lowestconcentration sample to 12.3% in the sample with high concentrations ofall four amino acids.

Control of Acidic Species Through Cell Culture with Increased Arginineand Lysine and Choice of Harvest Criterion and/or Modulation of pH

The increase of the amino acid (arginine, lysine) concentration in basalmedia may also be combined with choice of when to harvest a culture toachieve optimal reduction in total acidic species. In this example, astudy was carried out in 3 L bioreactors with cell line 1 (producingadalimumab) in media 1. Two sets of conditions were tested: Controlcondition (Arginine 1 g/l, Lysine 1 g/l); Test condition 1 (Arginine 3g/l, Lysine 5 g/l). Cell growth, viability and titer profiles werecomparable between the conditions (FIG. 63, 64, 65). A small amount ofcell culture harvests were collected every day from day 4 to day 10 fromeach of the reactors and submitted for protein A purification and WCX-10analysis. The percentage of acidic species in the control conditionincreased from 12.1% (on day 4) to 24.6% (on day 10) (FIG. 66). Thepercentage of acidic species in the test condition 1 was lower than thatobserved in the control condition at each corresponding culture day. Thepercentage of acidic species in the test condition also increased from8.7% (day 4) to 18.8% (day 10). The rate of increase in acidic specieswith culture duration also correlated with the drop in viability forboth conditions, with a sharp increase on day 8, Thus, along withincreasing arginine and lysine concentrations in culture media, choiceof harvest day/harvest viability can be used in combination to achieve adesired acidic species reduction.

The increase of the amino acid (arginine, lysine) concentration in basalmedia may be combined with process pH modulation to achieve furtherreduction in total acidic species. In this example, a study was carriedout in 3 L bioreactors with cell line 1 (producing adalimumab) inmedia 1. Three sets of conditions were tested in duplicates: Controlcondition (Arginine (1 g/l), Lysine (1 g/l), pH 7.1->6.9 in 3 days, pH6.9 thereafter); Test condition 1 (Arginine (3 g/l), Lysine (3 g/l), pH7.1->6.9 in 3 days, pH 6.9 thereafter); Test condition 2 (Arginine (30),Lysine (3 g/l), pH 7.1->6.8 in 3 days, pH 6,8 thereafter). In comparisonto the control, a slight decrease in VCD profile and harvest titer wasobserved for condition 2 (FIG. 67, 68, 69). The cultures were harvestedwhen the viability was less than 50% and the culture harvests weresubmitted for protein A and WCX-10 analysis. The percentage of acidicspecies in the control sample was 19.1%. The percentage of acidicspecies was reduced to 14.3% in test condition 1 and to 12.8% in testcondition 2 (FIG. 70). Thus, this demonstrates that the increase ofamino acid concentration along with choice of lower final process pH canbe used in combination for further reducing the extent of acidicspecies.

Effect of Supplementation of CaCl₂ to Cell Culture Media

The addition of calcium chloride was tested in several experimentalsystems covering multiple cell lines, media and monoclonal antibodies.Following is a detailed description of two representative experimentswhere two different cell lines were cultured in a chemically definedmedia (media 1) for the production of adalimumab.

Cell line 2 was cultured in media 1 with different concentrations ofcalcium (0.14, 0.84 and 1.54 mM). The cultures were performed in shakeflasks in batch format with only glucose feed as described in thematerials and methods. The cells grew to maximum viable cell densities(VCD) in the range of 22-24.5×10⁶ cells/ml for the different conditionstested. The viable cell density and viability profiles for all testconditions were comparable (FIG. 71, 72). On Day 10 of culture sampleswere collected for titer analysis (FIG. 73). The titers for allconditions were comparable. On Day 10 duplicate shake flasks wereharvested for each condition and then subsequently analyzed using WCX-10post protein A purification and the percentages of total peak(s) areacorresponding to the acidic species were quantified (FIG. 74). Thepercentage of acidic species in the 0.14 mM calcium condition was 23.8%.In the sample with the highest tested concentration of calcium in thisexperiment (1.54 mM), the percentage of acidic species was reduced to21.6%. A dose dependent decrease in acidic species was observed in testconditions with increased calcium concentration.

Cell line 3 was cultured in media 1 with different total concentrationsof calcium (0.14, 0.49, 0.84, 1.19, 1.54, 1.89 g/l). The cultures wereperformed in shake flasks in batch format with only glucose feed asdescribed in the materials and methods. The cells grew to maximum viablecell densities (VCD) in the range of 9.5-10.5×10⁶ cells/ml for thedifferent conditions tested. The viable cell density and viabilityprofiles for all test conditions were comparable (FIG. 75, 76). On Day11 of culture, samples were collected for titer analysis. The harvesttiters for all conditions were comparable (FIG. 77). On Day 11 ofculture, duplicate shake flasks for each of the conditions wereharvested and then subsequently analyzed using WCX-10 post protein Apurification and the percentages of total peak(s) area corresponding tothe acidic species were quantified (FIG. 78). The percentage of acidicspecies in the 0.14 mM calcium condition was 23.7%. In the sample withthe highest tested concentration of calcium in this experiment (1.89mM), the percentage of acidic species was reduced to 20.7%. A dosedependent decrease in acidic species was observed in test conditionswith increased calcium concentration.

Additional experiments were performed with multiple cell lines inchemically defined or hydrolysate based media to evaluate the wide rangeof applicability of this method. The experimental setup for each ofthese experiments was similar to that described in section above and inthe materials and methods section. The summaries of results of thedifferent experiments performed for adalimumab are summarized in FIGS.79, 80 and 81. A reduction in acidic species with increased calciumconcentration was also observed in each case.

In addition to adalimumab, the utility of this method for acidic speciesreduction was also demonstrated for processes involving two other mABs.The experimental setup for each of these experiments was similar to thatdescribed in section above. The dose dependent reduction of acidicspecies with ornithine addition for experiments corresponding to eachmAB is summarized in FIGS. 82, 83. For mAB1, a small yet significantacidic species reduction from 15.4% (0.14 mM calcium sample) to 11.8%(1.54 mM calcium chloride supplemented sample) was observed. For mAB2, alarger dose dependent reduction from 28.9% (0.14 mM calcium sample) to23.1% (1,40 mM calcium chloride supplemented sample) was observed.

Effect of Increased Concentration of Arginine, Lysine, Calcium Chloride,Niacinamide in Combination

In this experiment, the effect of the combined use of the amino acidsarginine, lysine, inorganic salt calcium chloride and vitaminniacinamide for acidic species reduction was evaluated.

The experiment described here was performed using cell line 2 (producingadalimumab) in chemically defined media (media 1) supplemented with 3%(v/v) PFCHO (proprietary chemically defined medium formulation fromSAFC). A central composite DOE experimental design was used in thisexperiment. The basal media for each condition was supplemented withdifferent concentrations of the four supplements. Cell cultures werecarried out in duplicates for each condition. Upon harvest, WCX-10analysis was performed post protein A purification. In Table 3, theexperimental conditions from DOE design, including the concentration ofeach component supplemented, and the % total acidic species (or AR)obtained for each condition is summarized. Reduction of acidic speciesthrough the increased concentration of these components in combinationwas observed. For instance, condition (#24), where all four componentswere at their maximum concentration, the % total AR was reported to bereduced to 9.7%. Using the data from the experiment, a model predictingthe effects of addition of these components to media for AR reduction(R²: 0.92, P<0.0001) is described in FIG. 84. The model predicted acontribution from each of the four components towards acidic speciesreduction. It may be also possible to utilize this model to predict thechoice of concentrations of these different components to the media, inorder to achieve a target reduction in total AR.

TABLE 3 Experimental design and summary for the combined addition ofarginine, lysine, calcium chloride and niacinamide Calcium ArginineLysine Chloride Niacinamide % Total Conditions (g/l) (g/l) (mM) (mM) AR1 0.0 4.0 0.7 0.8 13.0 2 0.0 6.0 1.4 0.0 12.6 3 4.0 2.0 0 1.6 12.3 4 4.06.0 0 1.6 11.6 5 2.0 4.0 0.7 0.8 11.2 6 0.0 6.0 0 0.0 15.0 7 0.0 6.0 1.41.6 10.7 8 0.0 2.0 0 0.0 16.7 9 2.0 4.0 0.7 0.8 11.0 10 4.0 6.0 1.4 1.611.0 11 2.0 2.0 0.7 0.8 12.9 12 2.0 4.0 1.4 0.8 11.1 13 0.0 6.0 0 1.613.2 14 4.0 2.0 0 0.0 12.3 15 2.0 4.0 0.7 0.0 13.0 16 2.0 4.0 0.7 1.611.4 17 0.0 2.0 1.4 1.6 12.0 18 2.0 4.0 0 0.8 12.0 19 4.0 4.0 0.7 0.812.0 20 0.0 2.0 1.4 0.0 14.0 21 4.0 6.0 1.4 0.0 11.0 22 0.0 2.0 0 1.613.6 23 2.0 6.0 0.7 0.8 11.0 24 4.0 2.0 1.4 1.6 9.7 25 4.0 6.0 0 0.011.8 26 4.0 2.0 1.4 0.0 10.4 27 2.0 4.0 0 0.0 12.7

Use of Niacinamide Supplementation to Cell Culture Media for AcidicSpecies Reduction

In addition to the use of niacinamide in combination with othersupplements described in the previous section, niacinamide addition mayalso be used independent of the other supplements as demonstrated in theexperiments below for two mAbs: adalimumab and mAb1.

For the experiment corresponding to adalimumab, Cell line 1 was culturedin media 1 supplemented with different amounts of niacinamide (0, 0.2,0.4, 0.8 and 1.6 mM). The cultures were performed in shake flasks inbatch format with only glucose feed as described in the materials andmethods. The cells grew to maximum viable cell densities (VCD) in therange of 8.5-11×10⁶ cells/ml for the different conditions tested. Aslight decrease in the viable cell density profile was observed with themaximum niacinamide supplementation (1.6 mM for this experiment) (FIG.85). The viability profile for the test conditions were comparable (FIG.86). On Day 12 of culture, samples were collected for titer analysis.The titers for all conditions were comparable (FIG. 87). On Day 11 andday 12, duplicate shake flasks were harvested for each condition andthen subsequently analyzed using WCX-10 post protein A purification andthe percentages of total peak(s) area corresponding to the acidicspecies were quantified (FIG. 88, 89). The percentage of acidic speciesin the day 10 control sample (without niacinamide supplementation) was19.6%. In the day 10 sample with the highest tested concentration ofniacinamide in this experiment (1.6 mM), the percentage of acidicspecies was reduced to 15.9%. Similar acidic species reduction withniacinamide supplementation was also observed in the day 12 samples.

For the experiment corresponding to mAb2, a mAB2 producing cell line wascultured in media 1 supplemented with different amounts of niacinamide(0, 0.1, 0.5, 1.0, 3.0 and 6.0 mM). The cultures were performed in shakeflasks in batch format with only glucose feed as described in thematerials and methods. The cells grew to maximum viable cell densities(VCD) in the range of 14-21.5×10⁶ cells/ml for the different conditionstested. A slight decrease in the viable cell density profile wasobserved for the conditions with 3.0 mM and 6.0 mM niacinamideconcentrations (FIG. 90). The viability profiles for all test conditionswere comparable (FIG. 91). On Day 12 of culture samples were collectedfor titer analysis (FIG. 92). The titers for all conditions werecomparable. On Day 12 duplicate shake flasks were harvested for eachcondition and then subsequently analyzed using WCX-10 post protein Apurification and the percentages of total peak(s) area corresponding tothe acidic species were quantified (FIG. 93). The percentage of acidicspecies in the control sample (without niacinamide supplementation) was27.0%. In the sample with the highest tested concentration ofniacinamide in this experiment (6.0 mM), the percentage of acidicspecies was reduced to 19.8%. A dose dependent decrease in acidicspecies was observed in test conditions with niacinamidesupplementation.

Types of Acidic Species Variants Reduced by Supplementation of CultureMedium with Additives

The addition of medium additives may be used to specifically reduceparticular acidic variants within the larger fraction of total acidicspecies. In Table 4, a summary of the extent of some of the sub-speciesof the acidic species fraction have been presented for a representativeset of experiments for adalimumab. Along with the reduction in totalacidic species, the methods presented in this section may also be usedfor reduction of sub-species that include, but not limited to, AR1, AR2and MGO (methylglyoxal) modified product variants.

TABLE 4 Summary of types of acidic species variants reduced in culturessupplemented with medium additives Sample % MGO modified species LIGHTCHAIN HEAVY CHAIN % AR % AR1 % AR2 Arg 30 Arg 93 Arg 108 Arg 16 (19) Arg259 Arg 359 Arg 420 TOTAL Control 26.9 9.7 17.3 1.63 1.21 0.33 0.6 0.063.98 3.31 11.1 Lysine (10 g/l) 15.0 4.5 10.4 1.29 0.91 0 0.46 0.04 1.772.09 6.56 Histidine (10 g/l) 14.7 5.3 9.4 1.21 0.61 0 0.49 0.02 1.421.47 5.22 Ornithine (10 g/l) 16.5 4.4 12.1 1.17 0.71 0 0.37 0.03 1.111.29 4.68 Control 22.5 7.5 15.0 1.13 0.69 0 0.17 0.02 0.03 0 2.04Arginine (8 g/l) 17.1 4.6 12.5 1.05 0.63 0 0.16 0.04 0.04 0 1.92 Control23.1 6.6 16.6 1.43 0.82 0 0.38 0.05 1 1.35 5.03 Calcium Chloride 20.85.9 14.9 1.28 0.83 0 0.2 0.04 1.07 1.52 4.94 (1.75 mM)

6.1.3 Conclusion

The different experiments above demonstrate that supplementation of cellculture medium with supplemental amounts of amino acids, calciumchloride and niacinamide enhances product quality by decreasing theamount of acidic species in the culture harvest. The amino acidsincluded in the study were arginine, lysine, ornithine and histidine andbelong to group of amino acids that are basic. The study coveredexamples from multiple cell lines/molecules, in shake flasks andbioreactors and in batch and fed-batch culture formats. A dose dependenteffect in the extent of reduction of acidic species with increasingconcentrations of the supplements was observed. In addition, thepossibility to supplement these medium additives individually or insuitable combinations for acidic species reduction was alsodemonstrated.

6.2 Method for reducing the extent of acidic species in cell culture byadjusting Process Parameters

6.2.1 Materials and Methods

Cell Source and Adaptation Cultures

Two adalimumab producing CHO cell lines and a mAB2 producing cell linewere employed in the studies covered here. Upon thaw, adalimumabproducing cell line 3 was cultured in chemically defined growth media(media 1) in a combination of vented shake flasks on a shaker platform@140 rpm and 20 L wave bags. Cultures were propagated in a 36° C., 5%CO₂ incubator to obtain the required number of cells to be able toinitiate production stage cultures.

Upon thaw, adalimumab producing cell line 1 was cultured in ahydrolysate based growth media (media 2) in a combination of ventedshake flasks on a shaker platform @ 110 rpm and 20 L wavebags in a 35°C., 5% CO₂ incubator. In some cases, the culture might be transferredinto a seed reactor with pH 73, 35° C. and 30% DO. The culture would beadapted to either media 1 or media 2 by propagated in a 10 L or 20 Lwavebag for 7-13 days with one or two passages before initiatingproduction stage cultures.

Upon thaw, mAb2 producing cells were cultured in media 1 in acombination of vented non-baffled shake flasks (Corning) on a shakerplatform at 140 RPM and 20 L wave bags (GE). Cultures were propagated ina 35° C., 5% CO₂ incubator to obtain the required number of cells to beable to initiate production stage cultures.

Cell Culture Media

Media 1, the chemical defined growth or production media, was preparedfrom basal IVGN CD media (proprietary formulation). For preparation ofthe IVGN CD media formulation, the proprietary media was supplementedwith L-glutamine, sodium bicarbonate, sodium chloride, and methotrexatesolution. Production media consisted of all the components in the growthmedium, excluding methotrexate. For cell line 1 and mAb2, the medium wasalso supplemented with insulin, In addition, 10 mM or 5 mM of Galactose(Sigma, G5388) and 0.2 μM or 10 μM of Manganese (Sigma, M1787) weresupplemented into production medium for cell line 3 or 1, respectively.Osmolality was adjusted by the concentration of sodium chloride. Allmedia was filtered through filter systems (0.22 μm PES) and stored at 4°C. until usage.

Media 2 is the hydrolysate based media, which contains basal proprietarymedia, Bacto TC Yeastolate and Phytone Peptone.

Production Cultures

Production cultures were initiated in 3 L Bioreactors (Applikon). Thebioreactors (1.5-2.0 L working volume) were run at the followingconditions (except for the different experimental conditions): 35° C.,30% DO (dissolved oxygen), 200 rpm, pH profile from 7.1 to 6.9 in threedays and pH 6.9 thereafter. In all experiments, the cells weretransferred from the wavebag to the production stage at a split ratio of1:5.6 (except mAb2 with a ratio of 1:5). When the media glucoseconcentration reduced to less than 3 g/L, approximately 1.25% (v/v) of40% glucose stock solution was fed

The harvest procedure of reactors involved centrifugation of the culturesample at 3,000 RPM for 30 min and storage of supernatant in PETGbottles at −80° C. before submission for protein A purification andWCX-10 analysis.

WCX-10 Assay

The acidic species and other charge variants present in cell cultureharvest samples were quantified. Cation exchange chromatography wasperformed on a Dionex ProPac WCX-10, Analytical column (Dionex, CA). Foradalimumab producing cell lines, a Shimadzu LC 10A HPLC system was usedas the HPLC. The mobile phases used were 10 mM Sodium Phosphate dibasicpH 7.5 (Mobile phase A) and 10 mM Sodium Phosphate dibasic, 500 mMSodium Chloride pH 5.5 (Mobile phase B). A binary gradient (94% A, 6% B:0-20 min; 84% A, 16% B: 20-22 min; 0% A, 100% B: 22-28 min; 94% A, 6% B:28-34 min) was used with detection at 280 nm. The WCX-10 method used formAb B used different buffers. The mobile phases used were 20 mM(4-Morpholino) ethanesulfonic Acid Monohydrate (MES) pH 6.5 (Mobilephase A) and 20 mM MES, 500 mM Sodium Chloride pH 6.5 (Mobile phase B).An optimized gradient (minute/% B): 0/3, 1/3, 46/21, 47/100, 52/100,53/3, 58/3 was used with detection at 280 nm.

Quantitation is based on the relative area percent of detected peaks.The peaks that elute at relative residence time earlier than the mainpeak corresponding to the drug product are together represented as theacidic peaks.

6.2.2 Results

Effect of Process pH in Media 1 with Cell Line 1

Five different pH conditions were assessed in this study: 7.1, 7.0, 6.9,6.8 and 6.7. The cultures were started at pH set point of 7.1; then wereramped down to the target pH set points within 4 days. All culturesreached the same maximum viable cell density on day 8, except for theculture at pH 6.7 condition, in which the maximum cell density was muchlower than the other cultures (FIG. 94). In addition, the viability ofthe culture at pH 7.1 and pH 7.0 dropped much earlier than the othercultures. The viability of cultures at pH 7.1 and pH 7.0 were 38% and54% on day 10, respectively; while the viability of the cultures atlower pH (including pH 6.9, 6.8 and 6.7) was above 70% on the same day(FIG. 95). Samples taken in the last three days of the cultures weremeasured for IgG concentration. The titer of each tested conditionincreased corresponding to the decrease in pH, from 1.2 g/L in the pH7.1 condition to 1.8 g/L in the pH 6.8 condition; however, product titerwas not continued to increase at pH 6.7 (1.6 g/L) (FIG. 96). Thecultures were harvested either on day 10 or on day 12. The harvest wasprotein A purified, then analyzed using WCX-10. The resulting peak areasfrom WCX-10 analysis were quantified (FIG. 97). The percentage of acidicspecies decreased corresponding to the decrease in pH, from 56.0% in thepH 7.1 condition to 14.0% in the pH 6.7 condition. Since the cultures atpH 6.9, 6.8 and 6.7 were at 70% viability on day 10, additional sampleswere taken on day 12 for these cultures, when viability reached ˜50%.WCX-10 analysis was also performed for these samples. The percentage ofacidic species on day 12 was increased for these three conditions (i.e.,pH 6.9, 6.8 and 6.7) comparing to day 10; however, the increase in thepercentage of acidic species was smaller at lower pH. The percentage ofacidic species increased 18.8% (pH 6.9), 8.1% (pH6.8) and 3.5% (pH6.7),respectively from day 10 (70% viability) to day 12 (50% viability).Therefore, the percentage of acidic species was lower at lower pH on day12 too. The percent acidic species decreased with decrease in pH from39.1% in the pH 6.9 condition to 17.5% in the pH6.7 condition, for atotal reduction of 21.6%.

The effect of process pH to specifically reduce particular acidicvariants within the larger fraction of total acidic species was alsoevaluated. In Table 5, a summary of the extent of some of thesub-species of the acidic species fraction have been presented. Alongwith the reduction in total acidic species, the methods presented inthis section may also be used for reduction of sub-species that include,but not limited to, AR1, AR2 and MGO (methylglyoxal) modified productvariants.

TABLE 5 Effect of process pH on reduction of sub-species of acidicvariants Sample % MGO modified species LIGHT CHAIN HEAVY CHAIN Final pH% AR % AR1 % AR2 Arg 30 Arg 93 Arg 108 Arg 16 (19) Arg 259 Arg 359 Arg420 TOTAL 7.1 56.0 32.8 23.3 26.1 10.6 0.2 6.1 2.7 3.5 0.5 49.7 6.9 39.118.9 20.2 9.5 3.8 0.0 2.2 0.9 1.2 0.2 18.8 6.7 17.5 5.2 12.2 1.2 0.5 0.00.2 0.1 0.1 0.0 2.0

Effect of Process pH in Media 2 with Cell Line 1,

Three different pH conditions were assessed in this study: 7.0, 6.9, and6.8. The cultures were started at pH of 7.1; then were ramped down tothe target pH set points within 3 days of culture. The viable celldensity and viability were comparable across the different pH set pointsuntil day 8. After day 8, the viable cell density and viability wereslightly higher with lower pH set points (FIGS. 98 and 99). The cultureswere harvested on ˜50% viability. The product titer was slightly higherat pH 6.8 comparing to pH 6.9 and 7.0 (FIG. 100). The resulting peakareas from WCX-10 analysis were quantified (FIG. 101). The percentage ofacidic species decreased with decrease in pH from 20.7% in the pH 7.0condition to 18.0% in the pH6.8 condition, for a total reduction of2.7%.

Effect of Process pH in Media 1 with Cell Line 3

Five different pH conditions were assessed in this study: 7.1 7.0, 6,9,6.8, and 6.7.

The cultures were started at pH set point of 7.1; then were ramped downto the target pH set points within 4 days of culture. The pH set pointsshowed significant effect on the cell growth and viability with thiscell line and media. Cell density was lower at higher pH and viabilityalso dropped earlier at higher pH (FIGS. 102 and 103). The cells wereharvested either on day 10 or when viability dropped to equal or lessthan 50%. The titer was slightly increased as the pH was reduced,reached the highest titer at pH 6.8 condition (FIG. 104). The resultingpeak areas from WCX-10 analysis were quantified (FIG. 105). The percentacidic species decreased with decrease in pH from 29.7% in the pH 7.1condition to 21.5% in the pH6.7 condition, for a total reduction of8.2%.

6.2.3 Conclusion

The experiments described in the instant Example demonstrate thataltering cell culture process parameters on-line can be used tomodulate/reduce the acidic species of a protein of interest, e.g., theantibody adalimumab or mAB2. For example, a decrease in final pH setpoints can lead to reductions in Acidic Regions.

6.3 Method for Reducing Acidic Species in Cell Culture by the Additionof Amino Acids to Clarified Cell Culture Harvest and by Modifying the pHof the Clarified Harvest

The present study describes a process for reducing and controllinglevels of acidic species in antibody preparations. Specifically, theinvention provides a method for reducing the acidic variant content inclarified harvest, as well as a method for reducing the formation rateof acidic species in clarified harvest. The method involves addingadditives like various amino acids to clarified harvest or adjusting thepH of the clarified harvest using acidic substances.

6.3.1 Materials and methods

Clarified Harvest Material

Different batches of adalimumab clarified harvest material were employedin the following experiments described below. Clarified harvest isliquid material containing a monoclonal antibody of interest that hasbeen extracted from a fermentation bioreactor after undergoingcentrifugation to remove large solid particles and subsequent filtrationto remove finer solid particles and impurities from the material.Clarified harvest was used for low pH treatment studies describedherein. Clarified harvest was also used for the experiments to study theeffect of amino acid concentration on the presence of acidic species inclarified harvest, and for acid type-pH treatment studies describedherein. Different batches of mAB-B and mAb-C clarified harvest materialwere employed for experiments to study the effect of amino acid and lowpH treatment studies on the presence of acidic species described herein.

Preparation of Study Materials

The clarified harvest material was first adjusted to pH 4 using 3Mcitric acid. The material at pH 4 was then agitated for 60 minutesbefore adjusting the pH to a target pH of 5, 6 or 7 with 3M sodiumhydroxide. The material was then agitated for a further 60 minutes. Thesamples were then subjected to centrifugation at 7300×g for 15 minutesin a Sorvall Evolution RC with an SLA-3000 centrifuge bowl. Thesupernatants obtained from the centrifuged material were then depthfiltered using B1HC depth filters (Millipore) followed by 0.22 μmsterile filters. The filtrates of different pH were then subjected toholding for different period of time for evaluating the formation rateof acidic variants. After the holding, the material was purified withProtein A affinity column and the eluate was sampled and analyzed usingthe WCX 10 method. The preparation scheme is shown below in FIG. 106.

The material to study the effect of arginine on acidic species wasprepared in two ways. For lower target arginine concentrations of 5 mM,10 mM, 30 mM and 100 mM, they were made by adding the appropriate amountof 0.5M arginine stock buffer at pH 7 (pH adjusted with acetic acid) toattain the target arginine concentrations needed. For higher targetarginine concentrations of 50 mM, 100 mM, 300 mM, 500 mM, 760 mM, 1M and2M, they were made by adding the appropriate amount of arginine (solid)to the samples to attain the target arginine concentrations, withsubsequent titration to a final pH of 7 using glacial acetic acid.Arginine was adjusted to a final concentration of 100 mM using the twomethods to determine if the method of preparation would result indifferent effects. For all the experiments, following the arginineaddition, treated clarified harvests were held at room temperature forthe indicated duration followed by purification with Protein A columnand analysis of charge variants. This study provided two results; (1)data of samples from Day 0 gave the effects of arginine on reducingacidic species in clarified harvest, (2) data of samples with differentholding days gave effect of arginine on reducing the formation rate ofacidic species. The preparation scheme is shown in FIG. 107.

The material to study the effect of histidine was prepared with targetconcentrations of 5 mM, 10 mM, 30 mM 50 mM, 100 mM, 200 mM and 250 mM.The samples were prepared by adding the appropriate amount of histidine(solid) to the samples to attain the target histidine concentrations,with subsequent titration to a final pH of 7 using glacial acetic acid.The sample preparation scheme is shown in FIG. 108.

The material to study the effect of Lysine was prepared with targetconcentrations of 5 mM, 10 mM, 30 mM 50 mM, 100 mM, 200 mM, 300 mM, 500mM and 1000 mM. The samples were prepared by adding the appropriateamount of lysine hydrochloride (solid) to the samples to attain thetarget Lysine concentrations, with subsequent titration to a final pH of7 using hydrochloric acid. The sample preparation scheme is shown belowin FIG. 109.

The material to study the effect of methionine was prepared with targetconcentrations of 5 mM, 10 mM, 30 mM 50 mM, 100 mM, 200 mM and 300 mM.The samples were prepared by adding the appropriate amount of methionine(solid) to the samples to attain the target methionine concentrations,with subsequent titration to a final pH of 7 using glacial acetic acid.The sample preparation scheme is shown in FIG. 110.

The material to study the effect of different amino acids was preparedwith different target concentrations for each of the 20 amino acidsevaluated as well as two controls using sodium acetate in place of anamino acid, and the other simply bringing the pH of the clarifiedharvest down to pH 7 using glacial acetic acid. The targetconcentrations for the amino acids are shown below in Table 6.

TABLE 6 Amino Acid Target Concentrations Concentration Amino Acid (mM)Alanine 100 Arginine 100 Asparagine 100 Aspartic Acid 30 Cysteine 100Glutamic Acid 30 Glutamine 100 Glycine 100 Histidine 100 Isoleucine 100Leucine 100 Lysine 100 Methionine 100 Phenylalanine 100 Proline 100Serine 100 Threonine 100 Tryptophan 30 Tyrosine 2 Valine 100 NaAc 100

The samples were prepared by adding the appropriate amount of amino acid(solid) to the samples to attain the target amino acid concentrations asshown in Table 6, with subsequent titration to a final pH of 7 usingglacial acetic acid. The sample preparation scheme is shown below inFIG. 111.

The material to study the effect of additives other than amino acids wasprepared with different target concentrations for each of the additivesevaluated as well as a control in which sodium hydroxide was used inplace of arginine to bring the pH of the material to pH 10 beforeneutralizing it back to pH 7 with glacial acetic acid. The targetconcentrations for the additives are shown below in Table 7.

TABLE 7 Alternative Additive Target Concentrations Additive Low ConcHigh Conc Sucrose 0.1M 1M Trehalose 0.1M 1M Mannitol   4% w/v 10% w/vGlycerol   1% v/v 10% v/v PEG   1% w/v  2% w/v Tween80 0.5% v/v  2% v/v

The samples were prepared by adding the appropriate amount of additiveto the samples to attain the target amino acid concentrations as shownin Table 2, with subsequent titration to a final pH of 7 using glacialacetic acid.

The material to study the effect of the aforementioned methods on CDMclarified harvest was prepared using the following scheme shown in FIG.112.

The in Ab B hydrolysate clarified harvest was used to study the effectof the aforementioned methods.

The mAb C hydrolysate clarified harvest was used to study the effect ofthe aforementioned methods.

Hold Studies for Treated Clarified Harvest

After the aforementioned sample preparations, the samples were placed inseparate sterile stainless steel containers for the purpose of holdingat either 4° C. or at room temperature. For each material, differentcontainers were used for each day of holding evaluated. For theacidified samples, the acidic variant compositions of the samples wereevaluated on days 0, 3, 7 and 14 of holding at either temperature. Forthe arginine containing materials, the acidic variant compositions ofthe samples were evaluated on days 0, 5 and 8 of holding at roomtemperature. For the histidine containing materials, the acidic variantcompositions of the samples were evaluated on days 0, 3 and 7 of holdingat room temperature.

Acid Type and pH Effects on Clarified Harvest

The effects of acid type, clarified harvest pH and arginine content onacidic variant reduction were evaluated in this study. The samples wereprepared in triplicates on 3 consecutive days to target arginineconcentrations of either 0 mM (no arginine added) or 500 mM, thentitrated with either glacial acetic acid, phosphoric acid, 3M citricacid or 6M hydrochloric acid to target pH values of either 5, 6 or 7.One other sample was prepared by adding a 2M arginine acetate pH 7 stockbuffer to clarified harvest to attain a target arginine concentration of500 mM. The sample preparation scheme is shown in FIG. 113.

Protein A Purification

Protein A purification of the samples was performed using a 5 mLrProtein A FF Hitrap column (GE Healthcare) at 10 g D2E7/1, resinloading and a operating flow rate of 3.4 mL/min. 5 column volumes (CVs)of equilibration (1×PBS pH 7.4) is followed by loading of the sample,then washing of the column with equilibration buffer to removenon-specifically bound impurities, followed by elution of the proteinwith 0.1M Acetic acid, 0.15M sodium chloride.

The eluate samples were collected and neutralized to pH 6.9-7.2 with 1MTris pH 9.5 at 45-75 minutes after collection. The samples were thenfrozen at −80° C. for at least one day before thawing and subjecting toWCX-10 analysis.

Effects Purification Method, Acid Concentration and Neutralization onClarified Harvest

The effects of purification methods with different types ofchromatography resins, acid concentration and pH neutralization onacidic variant reduction were evaluated in this study. The followingsamples were prepared, shown below in Table 8.

TABLE 8 Acid Concentration Sample Treatments Sample Treatment ControlNone 3M Citric Acid pH 6 Titrate to pH 6 with 3M Citric Acid 1M CitricAcid pH 6 Titrate to pH 6 with 1M Citric Acid Glacial Acetic Acid pH 6Titrate to pH 6 with Glacial Acetic Acid 3M Acetic Acid pH 6 Titrate topH 6 with 3M Acetic Acid 3M Citric Acid pH 5 Titrate to pH 5 with 3MCitric Acid 3M Acetic Acid pH 5 Titrate to pH 5 with 3M Acetic Acid 3MCitric Acid pH 5 to 7 Titrate to pH 5 with 3M Citric Acid, then 3M Tristo pH 7 3M Acetic Acid pH 5 to 7 Titrate to pH 5 with 3M Acetic Acid,then 3M Tris to pH 7

Each of the material made was then subjected to either Mabselect Sure orFractogel S capture in duplicate. The eluate samples are collected andneutralized to pH 6.9-7.2 with 1M Iris pH 9.5 at 45-75 minutes aftercollection. The samples are then frozen at −80° C. for at least one daybefore thawing and subjecting to WCX-10 analysis.

Charge Variant Analysis (WCX-10 Assay)

Cation exchange chromatography was performed on a 4 mm×250 mm DionexProPac WCX-10 Analytical column (Dionex, CA). A Shimadzu LC10A HPLCsystem was used to perform the HPLC assay. The mobile phases used were10 mM Sodium Phosphate dibasic pH 7.5 (Mobile phase A) and 10 mM SodiumPhosphate dibasic, 500 mM Sodium Chloride pH 5.5 (Mobile phase B). Abinary gradient (94% A, 6% B: 0-20 min; 84% A, 16% B: 20-22 min; 0% A,100% B: 22-28 min; 94% A, 6% B: 28-34 min) was used with detection at280 nm.

Quantitation is based on the relative area percent of detected peaks.The peaks that elute at relative residence time less than that of thedominant Lysine 0 peak are together represented as the acidic variantpeaks (AR).

6.3.2 Results

Effect of Low pH Treatment with Subsequent Neutralization

The results of the low pH treatment with subsequent neutralization areshown below in FIGS. 114 and 115. FIG. 115 shows that the low pHtreatment with subsequent neutralization to pH 5 or 6 reduces the rateof acidic variant formation over time. However, there is no significantreduction in initial acidic variant content as shown in FIG. 114.

Effect of Arginine Treatment

The results of the arginine treatment are shown in FIG. 116 and FIG.117. FIG. 116, 117 shows that the sample preparation method resulted indifferent levels of acidic species in clarified harvest. Adding a 0.5MArginine pH 7 stock buffer tends to increase acidic species, whileadding pure arginine with subsequent acetic acid titration to pH 7reduced acidic variants at arginine concentrations of greater than 100mM. Moreover, the effect due to treatment method is demonstrated whencomparing the two 100 mM arginine samples, which show an absolutedifference of 1% in acidic variants between the two methods.

FIG. 118 shows that the rate of acidic variant formation decreases withincreasing arginine concentration in clarified harvest, plateauing ataround concentrations of 500 mM arginine and higher. However, the twomethods of sample preparation does not result in significantly differentformation rate of acidic variants.

Effect of Histidine Treatment

The results of the histidine treatment are shown in FIG. 119 and FIG.120. Similar to arginine treatment effect, as shown in FIG. 128, whenhistidine was added to clarified harvest with subsequent pHneutralization with acetic acid, acidic variants were reduced athistidine concentrations higher than 50 mM. FIG. 120 shows that the rateof acidic variants formation decreases with increasing Histidineconcentration in clarified harvest, plateauing at around concentrationsof 200 mM Histidine and higher.

Effect of Lysine Treatment

The results of the lysine treatment are summarized in FIG. 121 and FIG.122. Similar to arginine treatment effect, as shown in FIG. 128, whenlysine was added to clarified harvest with subsequent pH neutralizationwith acetic acid, acidic variants were significantly reduced by ˜1% ormore. FIG. 132 shows that the rate of acidic variants formationdecreases with increasing lysine concentration in clarified harvest.

Effect of Methionine Treatment

The results of the methionine treatment are summarized below in FIGS.133 and 144. Similar to arginine treatment effect, as shown in FIG. 118,when methionine was added to clarified harvest with subsequent pHneutralization with acetic acid, acidic variants were significantlyreduced by ˜1% or more at concentrations of >10 mM. FIG. 124 shows thatthe rate of acidic variants formation is not affected significantly bymethionine presence in clarified harvest.

Effect of Other Amino Acid Treatment

The results of the treatments with the various amino acids aresummarized below in FIGS. 125 and 146. As shown in FIG. 125, theaddition of 14 amino acids including arginine, histidine, lysine andmethionine resulted in lower amounts of acidic variant content inclarified harvest. The addition of sodium acetate or the use of aceticacid also caused a reduction in acidic variant content as well. FIG. 126shows that the rate of acidic variants formation is reduced by severalamino acids including arginine, histidine, lysine, aspartic acid,glutamic acid, and leucine.

Effect of Alternative Additive Treatment

The results of the treatments with the other additives are summarizedbelow in FIGS. 127 and 128. As shown in FIG. 127, the addition of any ofthe additives did not result in lower acidic variant content in D2E7hydrolysate clarified harvest. However, FIG. 128 shows that the rate ofacidic variants formation is reduced by most of the additives.

Effect of Low pH/Arginine Treatment on D2E7 CDM Clarified Harvest

The results of CDM clarified harvest study are summarized below in FIGS.129 and 130. As shown in FIG. 129, low pH/arginine treatment did notresult in lower acidic variant content in D2E7 CDM clarified harvest.However, FIG. 130 shows that the rate of acidic variants formation isreduced significantly by all the treatments.

Effect of Low pH/Arginine Treatment on mAb B Hydrolysate ClarifiedHarvest

The results of mAb B hydrolysate clarified harvest study are summarizedbelow in FIGS. 131 and 132. As shown in FIGS. 131 and 132, lowpH/arginine treatment results in both lower acidic variant content andslower rates of acidic variants formation in mAb B hydrolysate clarifiedharvest.

Effect of Low pH/Arginine Treatment on mAb C Hydrolysate ClarifiedHarvest

The results of mAb C hydrolysate clarified harvest study are summarizedbelow in FIGS. 133 and 134. As shown in FIGS. 133 and 134, lowpH/arginine treatment results in both lower acidic variant content andslower rates of acidic variants formation in mAb C hydrolysate clarifiedharvest.

Effect of Acid Type and pH

The results obtained from the acid type-pH study are summarized in FIG.135. Greater acidic species reduction is obtained at lower pH. Arginineaddition also reduces acidic species content further, but not to asignificant extent when taking the high concentrations (500 mM) usedinto consideration. The results also show that acidic species reductionof ˜1% can be achieved with the usage of an arginine acetate stockbuffer, although using pure arginine powder with subsequent acidtitration performs slightly better. With regard to acid type used for pHadjustment, there were no significant differences between differentacids observed.

Effect of Purification Method, Acid Concentration and Neutralization

The results obtained from the study are summarized below in FIGS. 136,137, 138, and 139. FIGS. 136, 137 indicate that when the acid used is ofhigher concentration, there is an decrease in acidic variant content inhydrolysate clarified harvest as compared to a lower concentration acidbeing used. FIGS. 138, 139 show that when the clarified harvest issubjected to base neutralization to pH 7 after being treated with lowpH, there is an increase in acidic variant content. The figures alsoshow that the Fractogel resin is better able to clear acidic variantsthan Mabselect Sure.

6.3.3 Conclusion

Antibody acidic species in clarified harvest can be reduced by addingadditives such as arginine or histidine to clarified harvest atconcentrations of more than 100 mM and 50 mM, respectively. It can alsobe achieved by pH adjustment of the clarified harvest to pH 6 or pH 5.In addition, the rate of acidic variant formation can be reduced throughthe use of arginine or histidine in a concentration dependent manner, orby low pH treatment of the clarified harvest.

6.4 Method for Reducing Acidic Species in Cell Culture Use of aContinuous Media Perfusion Technology

As demonstrated in section 6.3, generation or formation of acidicspecies in the population of proteins may occur during the hold of theantibody in clarified harvest or spent media. Thus, the possibility ofenhanced stability of the product antibody or a reduction in acidicspecies generation was explored using a continuous/perfusion based cellculture technology, Control or reduction in the amount of acidic speciespresent in the population of proteins obtained at end of cell culturecan be accomplished by modifying the exchange rate of fresh medium intothe bioreactor (or removal of spent medium with product antibody out ofthe bioreactor).

6.4.1 Materials and Methods

Cell Source

One adalimumab producing CHO cell line was employed in the study coveredhere.

Upon thaw, the vial was cultured in a chemically defined growth media(media 1) in a series of vented shake flasks on a shaker platform at 110rpm in a 35° C., 5% CO₂ incubator. Cultures were propagated to obtain asufficient number of cells for inoculation of the perfusion cultibag.

Cell Culture Media

A chemically defined growth or production media was used in this study.For preparation of the media formulation, the proprietary media(Invitrogen) was supplemented with L-glutamine, sodium bicarbonate,sodium chloride, recombinant human insulin and methotrexate solution.Perfusion stage media consisted of all the components in the growthmedium, with the exception of a higher concentration of recombinanthuman insulin and the exclusion of methotrexate solution.

Perfusion Culture

The perfusion culture was carried out with the Sartorius BIOSTAT RM 20optical perfusion system (SN#00582|12) in a Sartorius Cultibag RM 10 Lperfusion pro 1.2 my (lot 1205-014) perfusion bag. The perfusion bag wasrun with a working culture volume of 1.5 L and operation conditions of;pH: 7.00, dissolved oxygen 30%, 25 rpm, 35° C., an air overlay of 0.3slpm and a CO₂ overlay of 15 sccm. pH control was initiated on day threeof the culture. pH was controlled with 0.5M sodium hydroxide and CO₂additions.

Perfusion was carried out by ‘harvesting’ spent culture through anintegrated 1.2 μm filter integrated into the perfusion cultibag. Freshmedia was added to the culture through a feed line at the same rate asthe harvest. Perfusion began on day four of the process at a rate of 1.0exchanges per day (ex/day). The perfusion rate was adjusted throughoutthe run to accommodate glucose needs, lactate accumulation and samplingplans. Perfusion cell-free harvest samples were collected at perfusionrates of 1.5, 3.0 and 6.0 exchange volumes/day on day 5-6 of perfusion.A fresh harvest bag was used for each harvest sample. The samples werethen purified using protein A and analyzed using WCX-10 assay.The perfusion culture was ended on day 8 of the process.

WCX-10 Assay

The acidic species and other charge variants present in cell cultureharvest samples were quantified. Cation exchange chromatography wasperformed on a Dionex ProPac WCX-10, Analytical column (Dionex, CA).

The mobile phases used were 10 mM Sodium Phosphate dibasic pH 7.5(Mobile phase A) and 10 mM Sodium Phosphate dibasic, 500 mM SodiumChloride pH 5.5 (Mobile phase B). A binary gradient (94% A, 6% B: 0-20min; 84% A, 16% B: 20-22 min; 0% A, 100% B: 22-28 min; 94% A, 6% B:28-34 min) was used with detection at 280 nm. The WCX-10 method used formAb2 samples used different buffers. The mobile phases used were 20 mM(4-Morpholino) ethanesulfonic to Acid Monohydrate (MES) pH 6.5 (Mobilephase A) and 20 mM MES, 500 mM Sodium Chloride pH 6.5 (Mobile phase B).An optimized gradient (minute/% B): 0/3, 1/3, 46/21, 47/100, 52/100,53/3, 58/3 was used with detection at 280 nm. Quantitation is based onthe relative area percent of detected peaks, as described above.

6.4.2 Results

Effect of Use of Perfusion Technology and Choice of Medium ExchangeRates on Acidic Species

Adalimumab producing cell line 1 was cultured in media 1 and thecultures were carried out as described in the materials and methods. Asdescribed in table 9, the exchange rates were modified over a period of24 hrs between day 5 and day 6 to explore the influence of mediumexchange rates on the extent of acidic species. At a continuous mediumexchange rate of 1.5 volumes/day, the product antibody in spent mediumwas collected in a harvest bag over a period of 17 hrs. The harvest bagwas then exchanged with a new bag and the old bag was transferred to 4C. Subsequently and in succession, the medium exchange rates wereincreased to 3 and 6 volumes/day and the product harvest was collectedover a time period of 5 and 2 hrs, respectively. After an overnight holdat 4 C, the three harvest samples were processed through protein A andanalyzed for acidic species using WCX-10. The percentage of acidicspecies in the sample with a medium exchange rate of 1.5 volumes/day was8.1%. In the sample with the highest tested exchange rate in thisexperiment (6 volumes/day), the percentage of acidic species was reducedto 6%. An exchange rate dependent reduction in acidic species wasobserved in the three samples (Table 9). Reductions in differentsub-species within the acidic variants (AR1 and AR2) were also noted. Anincrease in volumetric productivity, with exchange rate, was alsoobserved.

TABLE 9 Effect of medium exchange rates in a perfusion bioreactor onacidic species Harvest bag Exchange rate Exchange time Volumetric StartTime (no. of working (for collection in Productivity (day, hrs:min)volumes/day) harvest bag) (hrs) (mg/l-hr) % Total AR % AR1 % AR2 Day 5,16:00 1.5 17 10.94 8.1 2.0 6.1 Day 6, 10:25 3 5 39.80 6.9 1.7 5.2 Day 6,15:25 6 2 69.50 6.0 1.3 4.7

6.5. Utility of AR Reduction

The current invention provides a method for reducing acidic species fora given protein of interest. In this example adalimumab was preparedusing a combination of supplementation of arginine and lysine to cellculture as shown in this invention along with AEX and CEX purificationtechnologies (described in the U.S. patent application having attorneyreference no. 082254.0236) to produce a Low-AR and High-AR sample with afinal AR of 2,5% and 6.9%, respectively. Both samples were incubated ina controlled environment at 25° C. and 65% relative humidity for 10weeks, and the AR measured every two weeks. FIG. 142 shows the growth ofAR for each sample over the 10 week incubation. It is evident from FIG.142 the growth rate of AR is linear and similar between both the Low-ARand High-AR samples. Based on these results the reduced AR material canbe stored 3 fold longer before reaching the same AR level as the High-ARsample. This is a significant utility as this can be very beneficial instorage handling and use of the antibody or other proteins fortherapeutic use.

6.6 Process Combinations to Achieve Target % AR or AR Reductions

Upstream and Downstream process technologies, e.g., cell culture andchromatographic separations, of the inventions disclosed in thefollowing applications can be combined together or combined with methodsin the art to provide a final target AR value or achieve a % ARreduction, as well as to, in certain embodiments, reduce product relatedsubstances and/or process related impurities. Upstream methods for ARreduction include, but are not limited to those described in the instantapplication. Downstream methods for AR reduction include, but are notlimited to, those described in the U.S. patent application havingattorney reference no. 082254.0236. Exemplary technologies disclosed inthe referenced applications include, but are not limited to: cellculture additives & conditions; clarified harvest additives and pH/saltconditions; mixed mode media separations; anion exchange mediaseparations; and cation Exchange media separations.

The instant example demonstrates the combined effect of one or more ofthese technologies in achieving a target AR value or AR reduction,thereby facilitating the preparation of an antibody material having aspecific charge heterogeneity. Additional examples of combinations ofdownstream technologies and upstream technologies are provided in thereferenced applications.

In this example, the combination of upstream and downstream methodsinvolves the reduction of acidic species in 3 L bioreactor cell culturessupplemented with arginine (2 g/l) and lysine (4 g/l) as has beenpreviously demonstrated in the instant application. The results of thatstrategy are summarized in Table 10. The total acidic species wasreduced from 20.5% in the control sample to 10.2% in sample fromcultures that were supplemented with the additives. In this study,Adalimumab producing cell line 1 was cultured in media 1 (chemicallydefined media) supplemented with amino acid arginine (2 g/l) and lysine(4 g/l) in a 300 L bioreactor. On Day 12 of culture, the culture washarvested and then subsequently analyzed using WCX-10 post protein Apurification and the percentages of total peak(s) area corresponding tothe acidic species were quantified. The percentage of acidic species wasestimated to be 9.1% in the 300 L harvest sample

TABLE 10 AR levels achieved with use of upstream technologies 3 LBioreactor 300 L Bioreactor Arginine (2 g/l) + Arginine (2 g/l) +Control Lysine (4 g/l) Lysine (4 g/l) Total Total Total AR1(%) AR2(%) AR(%) AR1(%) AR2(%) AR (%) AR1(%) AR2(%) AR (%) 6.3 14.2 20.5 2.6 7.6 10.22.4 6.7 9.1

The material produced by the 300 L Bioreactor employing Arginine andLysine additions, that effectively reduced the AR levels to 9.1% waspurified using a downstream process employing Mixed Mode chromatographyas the primary AR Reduction method.

Adalimumab was purified by a Protein A chromatography step followed witha low pH viral inactivation step. The filtered viral inactivatedmaterial was buffer exchanged and loaded onto a Capto Adhere column. Theflowthrough of Capto Adhere material was then purified with a HIC columnwith bind/elute mode as well as Flow Through mode. As shown in Table 11,AR reduction was achieved primarily with MM step, with some contributionfrom other steps. The table also shows that additional product relatedsubstances such as aggregates and process related impurities such as HCPcan be effectively reduced employing these combined technologies.

TABLE 11 Complete Downstream Process Train with Protein A Capture - AR,HMW and HCP reduction Yield % AR % HMW Process (%) reduction reductionHCP LRF Clarified Harvest 97.0% n/a n/a n/a Prt-A Eluate Pool 89.6% 0.061.87 Viral Inactivated 99.7% No reduction 0.07 0.39 Filtrate MM FT pool91.9% 2.26 0.83 1.63 HIC (B/E) Eluate 90.1% 0.40 0.22 1.41 NanofiltrateFiltrate 90.7% No reduction No reduction 0.15 BDS (B/E) 102.0% Noreduction No reduction 0.22 HIC FT-pool 98.5% 0.16 0.23 0.46 VF(FT)Filtrate 96.1% No reduction No reduction 0.10 BDS (FT) 103.8% Noreduction No reduction No reduction

As is evident from the above example, the MM method further reduced theAR levels, by 2.26%. Therefore upstream technologies for reduction canbe combined with downstream technologies to achieve AR levels/ARreduction.

The present invention is not to be limited in scope by the specificembodiments described herein. Indeed, various modifications of theinvention in addition to those described herein will become apparent tothose skilled in the art from the foregoing description and theaccompanying figures. Such modifications are intended to fall within thescope of the appended claims.

Patents, patent applications, publications, product descriptions,GenBank Accession Numbers, and protocols that may be cited throughoutthis application, the disclosures of which are incorporated herein byreference in their entireties for all purposes. For example, but not byway of limitation, patent applications designated by the followingattorney docket numbers are incorporated herein by reference in theirentireties for all purposes: 082254.0104; 082254.0236; 082254.0238;082254.0242; and 082254.0243.

What is claimed is:
 1. A method for controlling acidic speciesheterogeneity in a population of a protein of interest produced by aculture of cells comprising implementing a change to a cell culturecondition whereby the change in the cell culture condition results incontrol of acidic species heterogeneity.
 2. The method of claim 1wherein the change to a cell culture condition is a change to the cellculture media.
 3. The method of claim 2 wherein the change to the cellculture media comprises an increase in the amount of an amino acidselected from the group consisting of arginine, lysine, ornithine,histidine, and combinations thereof, in the cell culture media.
 4. Themethod of claim 3 wherein the amino acid concentration is increased to aconcentration of between about 0.025 and 20 g/L.
 5. The method of claim2 wherein the change to the cell culture media comprises an increase inthe concentration of calcium in the cell culture media.
 6. The method ofclaim 5 wherein the calcium concentration is increased to aconcentration of between about 0.005 and 5 mM.
 7. The method of claim 5wherein the change to the cell culture media further comprises anincrease in the concentration of an amino acid selected from the groupconsisting of arginine, lysine, ornithine, histidine, and combinationsthereof, in the cell culture media.
 8. The method of claim 2 wherein thechange to the cell culture media comprises an increase in theconcentration of niacinamide, calcium, and at least one amino acid inthe cell culture media.
 9. The method of claim 8 wherein the change tothe cell culture media comprises an increase in the concentration of anamino acid selected from the group consisting of arginine, lysine,ornithine, histidine, and combinations thereof, in the cell culturemedia
 10. The method of claim 1 wherein the change to the cell culturecondition is a change selected from the group consisting of: the pH ofthe culture and the exchange rate of the culture.
 11. A method forcontrolling acidic species heterogeneity in a cell culture clarifiedharvest comprising a population of a protein of interest comprisingimplementing a change to a condition of the clarified harvest wherebythe change in the condition results in control of acidic speciesheterogeneity.
 12. The method of claim 11, wherein the change to acondition of the clarified harvest comprises addition of one or moreamino acids to the clarified harvest.
 13. The method of claim 12,wherein the one or more amino acids is selected from the groupconsisting of arginine, histidine, lysine, aspartic acid, glutamic acidand leucine and combinations thereof.
 14. The method of claim 11,wherein the change to a condition of the clarified harvest is anadjustment of the pH of the clarified harvest.
 15. The method of claim14 wherein the pH of the clarified harvest is adjusted to a pH ofbetween about 4.5 and 6.5.
 17. The method of claim 11 wherein the changeto a condition of the clarified harvest is an adjustment of the exchangerate.
 18. A pharmaceutical composition comprising an antibodypreparation with reduced of acidic species heterogeneity and apharmaceutically acceptable carrier.
 19. The pharmaceutical compositionof claim 18, wherein the antibody is an anti-TNFα antibody orantigen-binding portion thereof.
 20. The pharmaceutical composition ofclaim 18, wherein the composition is substantially free of acidicspecies heterogeneity.